the thing about using the ecu which came w/ your sr20det (w10 avenir i presume) is that the ecu is obd I while your car is wired for obd II (and it's a totally different engine w/ different management). the EASIEST (not cheapest) way to do the swap would be a jwt reprogrammed ecu. this makes everything pretty much plug and play, but you may have to swap over to the b14 se-r harness anyways. as far as using the w10 harness i don't know if that would be a very easy thing to do because it's not going to be compatible with the chassis harnesses.
as far as using an auto ecu in a manual car, it's no problem. i run an auto bluebird ecu in my 5speed g20 and there are absolutely no ill effects. good luck with the swap.
-kenji