Since you are considering a simple two layer feed forward network and have already pointed out 6 different things you need to consider to reduce classification errors, I just want to add one thing only and that is amount of training data. If you train a neural network with more data, it will work better. Note that, training with large amount of data is a key to get good outcome from neural networks, specially from deep neural networks.
Why the classification error goes up with more hidden neurons?
Answer is simple. Your model has over-fitted the training data and thus resulting in poor performance. Note that, if you increase the number of neurons in hidden layers, it would decrease training errors but increase testing errors.
In the following figure, see what happens with increased hidden layer size!
How may I vary the Learning Rate, Momentum, Training type, Epoch and Minimum Error in Matlab?
I am expecting you have already seen feed forward neural net in Matlab. You just need to manipulate the second parameter of the function feedforwardnet(hiddenSizes,trainFcn) which is trainFcn - a training function.
For example, if you want to use gradient descent with momentum and adaptive learning rate backpropagation, then use traingdx as the training function. You can also use traingda if you want to use gradient descent with adaptive learning rate backpropagation.
You can change all the required parameters of the function as you want. For example, if you want to use traingda, then you just need to follow the following two steps.
Example
net = feedforwardnet(3,'traingda');
net.trainParam.lr = 0.05; % setting the learning rate to 5%
net.trainParam.epochs = 2000 % setting number of epochs
Please see this - gradient descent with adaptive learning rate backpropagation and gradient descent with momentum and adaptive learning rate backpropagation.
