AVR-Chat

I recently upgraded a project from Mega16 to Mega164PA which is very similar to what you are doing.
You shouldn't have any problems except a lot of the register names need changing, and the timer setup is slightly different. If you are programming in assembler (which I seem to remember you aren't) then most of the registers have become sram addresses rather than io addresses so you have to use str-ldr instead of out-in instructions, in C this will happen automatically.

I don't use JTAG on it so can't help there.

-- 
Tim Mitchell