problem with zend module specific configuration

In the bootstrap, you can set your database connections:

protected function _initDb () {
    $config['my_db1'] = new Zend_Config_Ini(APPLICATION_PATH . '/configs/my_db1.ini');
    $config['my_db2'] = new Zend_Config_Ini(APPLICATION_PATH . '/configs/my_db2.ini');

    $my_db1 = new Plugin_Replication($config['my_db1']->toArray());
    $my_db1->query("SET CHARACTER SET utf8;");

    $my_db2 = new Plugin_Replication($config['my_db2']->toArray());
    $my_db2->query("SET CHARACTER SET utf8;");

    Zend_Db_Table::setDefaultAdapter($dmy_db1);
    Zend_Registry::set('my_db1', $my_db1);
    Zend_Registry::set('my_db2', $my_db2);
}

Each connection is specified in a separate .ini file in my case. I find this pretty intuitively organised. A database ini file does not require the resources.db.whatever names. Mine go like this:

[Master]
host = "xxx"
username = "xxx"
password = "xxx"
dbname = "xxx"
charset = utf8

[Slaves]
first.host = "xxx"
first.username = "xxx"
first.password = "xxx"
first.dbname = "xxx"
first.charset = utf8

second.host = "xxx"
second.username = "xxx"
second.password = "xxx"
second.dbname = "xxx"
second.charset = utf8

Once you have multiple databases set up like this, when creating a model (in any module you wish), you can inform ZF about the database you would like to use:

protected function _setupDatabaseAdapter() {
    $this->_db = Zend_Registry::get('my_db1');
}

This will be your default adapter. In case you need to use two databases in the same query, start your model's function with:

public function myAwesomeSqlQuery () {
    $db1 = $this->getAdapter()->getConfig(); //default adapter
    $db2 = Zend_Registry::get('my_db2')->getConfig(); //additional adapter

Now, you can write your query using the two databases this way:

$sql = $this
    ->select()
    ->setIntegrityCheck(false)
    ->from(array('col1' => $db1['dbname'].'.some_column'))
    ->join(array('col2' => $db2['dbname'].'.some_other_column')),'col1.id = col2.id')
;

As I suggested in a comment, you can also use module-specific bootstraps. The structure would go like this:

/application/
  -- /modules/
    -- /v1/
        -- /controllers/
        -- /views/
        -- /Bootstrap.php
    -- /v2/
        -- /controllers/
        -- /views/
        -- /Bootstrap.php

The module-specific bootstraps are constructed pretty much like any other bootstrap, but they affect the module in question. The class names are typically prefixed with the modules names, e.g.:

<?php
class V1_Bootstrap extends Zend_Application_Bootstrap_Bootstrap {
    ...
}

I generally try not to use module-specific bootstraps because they are all launched with each request (Zend Framework 2 is supposed to correct this), running functions that aren't necessary for your current module. Anyway, I found a module-specific bootstrap in one of my modules, which contains something like this:

class MyModule_Bootstrap extends Zend_Application_Bootstrap_Bootstrap {
    protected function _initLoggers () {
        $my_db1 = Zend_Registry::get('my_db1');
        $my_db2 = Zend_Registry::get('my_db2');
        $my_db1->setProfiler(new Zend_Db_Profiler_Firebug())->getProfiler()->setEnabled(true);
        $my_db2->setProfiler(new Zend_Db_Profiler_Firebug())->getProfiler()->setEnabled(true);

        $auth = Zend_Auth::getInstance();
        $columnMapping = array('priority' => 'priority' , 'message' => 'message' , 'timestamp' => 'timestamp' , 'username' => 'username');
        $logger = new Zend_Log(new Zend_Log_Writer_Db($my_db1, 'logs', $columnMapping));
        print_r($auth->getIdentity());
        if ($auth->hasIdentity())
            $logger->setEventItem('username', $auth->getIdentity()->username);
        Zend_Registry::set('logger', $logger);
    }

That's pretty much it. I hope it helps.

osebboy's solution is not configured to have a configuration file other than .ini. You have application.xml. It seems like the initial setup is incorrect depending on osebboy's solution.

I suggest that you download the source from his github and set it up that way. Also read his blog post about it.