Need lot GPIO pins on arduino mega - what are restrictions? I would like to use as much as possible GPIO pins on Arduino Mega especially with (mis)using pinMode(x,INPUT); and pinMode(x,INPUT_PULLUP); to achieve two things at the same time - drive something else by the pin weakly down or up and measure the logical level there with digitalRead(x) to detemine, if that "something else" is input, or outputting some logical level.

Also I need I2C, Serial over USB and nothing else.

On Arduino UNO/nano/micro/pro it works just fine for Digital pins (except D0/D1 (RX/TX), D13 (LED as strong pull-down), A4/A5 (I2C) and A6/A7 which are not digital IO). The problem is limited number of pins, so I bought ArduinoMega.

The question is - which pins can be used that way there?
So far I am aware of D0/D1 (RX/TX), D20/D21 (I2C) and D13 (LED). 
The rest (D2-D12, D14-D19, D22-D52 and A0-A15) seem aviable and usable.
Or I am missing something else?

Are there some libraries/objects I should disable to not interfere with my script?

Thank you.
All those pins should be available. But if you want to use Pin change interrupts, you have to check which pins are usable.