Backstore: Car was neglected, tranny fluid wasnt changed for 160k miles and yet ran 100%. Recently I dropped the pan and changed the filter/fluid with dex III/merc. Now I started to notice that after 30+mins of driving with a decent amount of stop n go driving that the shifts get noticeably harsher (especially if I accelerate slow) and there is a very faint whinnying sound.

I have decided to change the thermostat to the 180 one with hole drilled since we noticed the engine was running hotter after we changed it the first time while doing the intake manifold (we changed since we were already there but I guess we got a hotter one or something because ever since we noticed it runs alittle hotter)....This should keep the radiator cooler and hopefully help the tranny stay cooler

Which fluid should I get? Going to change the fluid as well since this harsh shifting happened after changing it.

your engine will not run right without the proper thermostat it should be 195. if its running hot try taking the fans out and back washing the rad with a hose and simple green. also the gauge may not be accurate, i try a ir temp gun and verify the temp gauge to that. as far as the fluid they are up to IV i think and gm says its for all vehicles

I think I would've flushed the tranny, since it was a very long time since the fluid/filter were changed. I agree with Justin about the proper thermostat for your vehicle, should keep it at 195.