I was doing some reading and it seems that you can change the pin locations the internal clock/timer are located on. For example Port B, and Port D on the 1284 have two timers, I'd like to move those to different pins. The reason I want to do this is because I'm building a all SMD board that I will be using the 1284 on and I wanted it to be 100% r3 compatible. Sadly with the clock/timers in their default location using optiboot code it doesn't allow me to have PWM on external int 1 and MOSI (pins d3, and D11).
If it's not possible then I think I'd like to use one of the pin's to control the ports physically attached to D3 & D11 to switch between PWM and other functionality compatibility. Obviously since I would be switching the physical attachment of the chip to different header locations this would mess up pin numbers, so I could have an alternative firmware. Thoughts on accomplishing this?