1 - those are the unused 5 volt and centertaps of the filament windings,
capping them is OK
2 - I would check the values of all of the resistors in that circuit, it
seems like some value is wrong - like R43, R44, R45 and R46 is
10K instead of 10 ohms
3 - Double check your wiring to the pots, you should have the ground
conductors at the switch end all connected together (with a ring of
wire so to speak) and that needs to go to the ground end of the
pots. You should try the amp with a simple "no pot' input and
see what you get.
What you didn't mention is this ... does the amp bias up properly,
since your question # 2 makes it sound like the bias is not right.
... tom
