my project is using up almost every pin on the Uno except for digital 0 and 1. I was wondering if there is a way to use these two pins for normal i/o by somehow disconnecting them from from the serial circuitry (I only need to talk serial through USB). Anyway to do this at all? Preferably via software?
You don't talk to the ATMega328P through USB. You talk to the 16U2 (or equivalent) through USB, and then it talks to the 328P through serial.
If you disconnect the serial connection between the two chips, then you have no serial communication, no USB communication, no way of programming the chip.
The only way to get access to D0 and D1 as normal IO is to not use any USB / Serial communication.
If you don't call Serial.begin() in your sketch then you can use the rx/tx pins as general I/O pins. Note that your sketch would no longer be able to communicate with the PC.