For the exhaust, you need to decide if you want to use the 16V manifold or the 20V. The 20V manifold is a much more efficient design, however involves more customization that the 16V. In both cases you will need to weld. I’ll cover both scenarios here.
Using the 20V Manifold
First of all, if you are reusing a C50 transmission you must use the 16V manifold as the 20V header will interfere with the starter. (Actually, someone just got done with his swap and says that the 20V header fits fine when using the starter on the exhaust side. So, YMMV.) If you have a C52 that has starter humps on both intake and exhaust sides you will need to move the starter to the intake side. I’ll leave the relocating exercise to you, as I don’t have much experience with it. However, I would recommend just using the C56 tranny as it is better geared for the high 20V powerband.
At any rate, you need to mate the 20V header with the MR2’s exhaust system. If you currently have a nice exhaust and don’t plan on replacing it, you will need to either extend your current downpipe to reach the header, or you will need to extend the header down to reach the downpipe. I believe there’s about a 2″ difference that needs to be made up. You will also need a custom flange to mate with the header. If you purchased a front clip, just use the flange off the downpipe.
I was building a whole new exhaust at the time, so I just reused the 20V downpipe and built the rest of the exhaust system off of it. The 20V downpipe is nice because it has a flexjoint in it, so that I didn’t have to incorporate a typical flexpipe. Here’s pics of my finished exhaust.
Using the 16V Manifold
If you use the 16V manifold (stock or a TRD) you will need to expand the ‘ears’ of the flange. Here’s pics courtesy of Dave Spinetti from his web page.
Ears cut off, notice the gap needed to be filled: