How long ago was the intake done? That could preclude a flush. It would have been done then. Is there a 'casting' date or mark on the intake? If it'* later than 99, you won't have to worry about that again.
Flushing the trans should run about 80 bucks, and would only be a possible problem if you're having fairly sever problems already. I'd suggest the best route would be to change the filter first, then go get a flush. Or maybe the other way around. Depends on whether it'* a reverse flush or not. This can be a huge benefit. Saved my *** a year ago, and I'm going to do it again soon. My shifts are a bit odd lately.
The 180° thermostat is commonly used to prolong the life of the plastic upper on the Vin K. It also tends to keep the intake charge cooler, and possibly extend the life of the other engine internals. There are probably thousands of cars running this thermostat now, with no ill-effects (not only is mine a 180, but it'* also got bypass holes drilled in it).