The way I see, I have three options worth considering:
- Rewrite the remote control receiver code to not use timer - able to time receiver accurately enough?
- Use a PC serial-based IR receiver, arduino connected via USB - Would require additional circuit board, but would open more control options such as a color chooser running on my PC. Lose remote control functionality when PC is off.
- Write a software PWM controller for LED's - way less precise control.