Replace glyph from font A with a glyph from font B in LuaLaTeX/Node?

If you want to use a callback and manually traverse the node list, then pre_shaping_filter (or possibly post_shaping_filter) is the callback that you're looking for.

%%%%%%%%%%%%%%%%%%%%%%
%%% Implementation %%%
%%%%%%%%%%%%%%%%%%%%%%

\documentclass{article}

\usepackage{luacode}
\begin{luacode*}
    -- Helper function to replace a node in a list with another node
    local function replace_node(head, old, new)
        local head, current = node.remove(head, old)
        if current then
            head, new = node.insert_before(head, current, new)
        else
            head, new = node.insert_after(head, node.slide(head), new)
        end
        return head, new
    end

    -- Helper function to memoize another function
    local function memoized(func)
        return setmetatable({}, { __index = function(cache, key)
            local ret = func(key, cache)
            cache[key] = ret
            return ret
        end })
    end

    -- Read and parse a font file
    local _define_font = memoized(function(name_size)
        local name, size = unpack(name_size:split(":"))
        local tfmdata = fonts.definers.read {
            lookup = "file",
            name = name,
            size = tonumber(size),
            features = {},
        }
        return font.define(tfmdata)
    end)

    local function define_font(name, size)
        return _define_font[name .. ":" .. tostring(size)]
    end

    -- Get a fonts name from its id
    local font_attributes = memoized(function(id)
        local tfmdata = font.getfont(id)
        return {
            (tfmdata.fullname or tfmdata.name or "unknown"):lower():split(".")[1],
            tfmdata.size,
            tfmdata.specification.features.raw,
        }
    end)

    -- The characters to substitute
    local code = utf8.codepoint

    local substitutions = {
        ["lmroman10-regular"] = {
            [code "a"]       = { "texgyreadventor-bold",       code "A" },
            [code "e"]       = { "texgyreadventor-bold",       code "E" },
            [code "i"]       = { "texgyreadventor-bold",       code "I" },
            [code "o"]       = { "texgyreadventor-bold",       code "O" },
            [code "u"]       = { "texgyreadventor-bold",       code "U" },
            [code "y"]       = { "texgyreadventor-bold",       code "Y" },
            [code "A"]       = { "texgyreadventor-bold",       code "a" },
            [code "E"]       = { "texgyreadventor-bold",       code "e" },
            [code "I"]       = { "texgyreadventor-bold",       code "i" },
            [code "O"]       = { "texgyreadventor-bold",       code "o" },
            [code "U"]       = { "texgyreadventor-bold",       code "u" },
            [code "Y"]       = { "texgyreadventor-bold",       code "y" },
            [code "h"]       = { "texgyrechorus-mediumitalic", code "H" },
            [code "l"]       = { "texgyrechorus-mediumitalic", code "L" },
            [code "m"]       = { "texgyrechorus-mediumitalic", code "M" },
            [code "n"]       = { "texgyrechorus-mediumitalic", code "N" },
            [code "r"]       = { "texgyrechorus-mediumitalic", code "R" },
            [code "H"]       = { "texgyrechorus-mediumitalic", code "h" },
            [code "L"]       = { "texgyrechorus-mediumitalic", code "l" },
            [code "M"]       = { "texgyrechorus-mediumitalic", code "m" },
            [code "N"]       = { "texgyrechorus-mediumitalic", code "n" },
            [code "R"]       = { "texgyrechorus-mediumitalic", code "r" },
        }
    }

    -- Define the callback function for character substitution
    luatexbase.add_to_callback("pre_shaping_filter", function(head)
        for n, char, font in node.traverse_glyph(head) do
            local font_name, font_size, font_features = unpack(font_attributes[font])

            local font_substitutions = substitutions[font_name]
            if not font_substitutions then goto continue end

            local substitution = font_substitutions[char]
            if not substitution then goto continue end

            if not font_features["example-substitution"] then goto continue end

            local substitute_font_name, substitute_char = unpack(substitution)
            local substitute_font = define_font(substitute_font_name, font_size)
            local glyph = node.copy(n)
            glyph.char = substitute_char
            glyph.font = substitute_font
            head = replace_node(head, n, glyph)

            ::continue::
        end
        return head
    end, "example-substitution")
\end{luacode*}


%%%%%%%%%%%%%%%%%%%%%
%%% Demonstration %%%
%%%%%%%%%%%%%%%%%%%%%

\usepackage{fontspec}
\setmainfont{Latin Modern Roman}

\pagestyle{empty}
\begin{document}
    The quick brown fox jumps over the lazy dog.

    {
        \addfontfeatures{RawFeature=+example-substitution}
        The quick brown fox jumps over the lazy dog.
    }
\end{document}

If you specifically want to only change the characters just as TeX is shipping out the page, after all the typesetting is finished, you can use pre_shipout_filter:

%%%%%%%%%%%%%%%%%%%%%%
%%% Implementation %%%
%%%%%%%%%%%%%%%%%%%%%%

\documentclass{article}

\usepackage{luacode}
\begin{luacode*}
    local TARGET_EX_HEIGHT = 0.430554 -- Based off of LM

    -- Helper function to replace a node in a list with another node
    local function replace_node(head, old, new)
        local head, current = node.remove(head, old)
        if current then
            head, new = node.insert_before(head, current, new)
        else
            head, new = node.insert_after(head, node.slide(head), new)
        end
        return head, new
    end

    -- Helper function to memoize another function
    local function memoized(func)
        return setmetatable({}, { __index = function(cache, key)
            local ret = func(key, cache)
            cache[key] = ret
            return ret
        end })
    end

    -- Read and parse a font file
    local _define_font = memoized(function(name_size)
        -- Get the parameters
        local name, size = unpack(name_size:split(":"))
        size = tonumber(size)
        local specification = {
            lookup = "file",
            name = name,
            size = tonumber(size),
            features = {},
        }

        -- Load the font data
        local tfmdata = fonts.definers.read(specification)

        -- Rescale by the ex-height
        local ex_height = tfmdata.parameters.x_height
        size = size^2 * TARGET_EX_HEIGHT / ex_height

        -- Reload the font with the new size
        specification.size = size
        tfmdata = fonts.definers.read(specification)

        return font.define(tfmdata)
    end)

    local function define_font(name, size)
        return _define_font[name .. ":" .. tostring(size)]
    end

    -- Get a fonts name from its id
    local font_attributes = memoized(function(id)
        local tfmdata = font.getfont(id)
        if not tfmdata then
            return { 0, {} }
        end
        return {
            tfmdata.size,
            ((tfmdata.specification or {}).features or {}).raw or {},
        }
    end)

    -- The fonts to use
    local font_names = {
        "texgyreadventor-bold",
        "texgyreadventor-bolditalic",
        "texgyreadventor-italic",
        "texgyreadventor-regular",
        "texgyrebonum-bold",
        "texgyrebonum-bolditalic",
        "texgyrebonum-italic",
        "texgyrebonum-regular",
        "texgyrechorus-mediumitalic",
        "texgyrecursor-bold",
        "texgyrecursor-bolditalic",
        "texgyrecursor-italic",
        "texgyrecursor-regular",
        "texgyreheros-bold",
        "texgyreheros-bolditalic",
        "texgyreheros-italic",
        "texgyreheros-regular",
        "texgyreheroscn-bold",
        "texgyreheroscn-bolditalic",
        "texgyreheroscn-italic",
        "texgyreheroscn-regular",
        "texgyrepagella-bold",
        "texgyrepagella-bolditalic",
        "texgyrepagella-italic",
        "texgyrepagella-regular",
        "texgyreschola-bold",
        "texgyreschola-bolditalic",
        "texgyreschola-italic",
        "texgyreschola-regular",
        "texgyretermes-bold",
        "texgyretermes-bolditalic",
        "texgyretermes-italic",
        "texgyretermes-regular",
    }

    math.randomseed(0)
    local function random_font()
        local name = font_names[math.random(#font_names)]
        return name
    end

    -- Define the hss node
    local hss = node.new("glue")
    hss.width = 0
    hss.stretch = 1
    hss.stretch_order = 2
    hss.shrink = 1
    hss.shrink_order = 2

    -- Define the callback function for character substitution
    local function recurse(head)
        for n in node.traverse(head) do
            if n.id == node.id("glyph") then
                -- Get the character and font
                local char, font = n.char, n.font
                local font_size, font_features = unpack(font_attributes[font])

                if not font_features["example-substitution"] then
                    goto continue
                end

                -- Create the substitute glyph
                local substitute_font = define_font(random_font(), font_size)
                local glyph = node.copy(n)
                glyph.font = substitute_font

                -- Box the glyph and adjust its dimensions
                glyph.next = node.copy(hss)
                local hbox = node.hpack(glyph)
                hbox.width = n.width
                hbox.height = n.height
                hbox.depth = n.depth

                -- Replace the node
                head, n = replace_node(head, n, hbox)
            elseif n.head or n.replace then
                if n.head then
                    n.head = recurse(n.head)
                end
                if n.replace then
                    n.pre     = recurse(n.pre)
                    n.post    = recurse(n.post)
                    n.replace = recurse(n.replace)
                end
            end
            ::continue::
        end
        return head
    end

    luatexbase.add_to_callback(
        "pre_output_filter", recurse, "example-substitution"
    )
\end{luacode*}


%%%%%%%%%%%%%%%%%%%%%
%%% Demonstration %%%
%%%%%%%%%%%%%%%%%%%%%

\usepackage{fontspec}
\setmainfont{Latin Modern Roman}

\usepackage[english]{babel}
\usepackage{blindtext}

\usepackage[landscape, letterpaper, margin=1cm]{geometry}
\usepackage{multicol}
\usepackage{microtype}
\pagestyle{empty}

\hyphenpenalty=-2000
\raggedcolumns

\begin{document}
    The quick brown fox jumps over the lazy dog.

    {
        \addfontfeatures{RawFeature=+example-substitution}
        The quick brown fox jumps over the lazy dog.
    }

    \clearpage

    \begin{multicols}{6}
        \Blindtext[4]
        \columnbreak

        \addfontfeatures{RawFeature={+example-substitution}}
        \Blindtext[4]
    \end{multicols}
\end{document}