Get some M6 bolts (1mm per thread pitch) to hold that intercooler cover down. They should line up with holes in the intercooler itself. One is already threaded, so you don't need a nut.
Definitely get a new throttle body inlet. Your options are new from toyota or check the "parts for sale" forum here and on
www.mr2oc.com to see if someone has one for sale or they're parting out a gen 2 3SGTE (in the MR2 world, their car is called a SW20 if it has the 2nd generation 3SGTE). You can also go to your local wrecker to see if they have one, but I doubt it. Wrecked MR2 turbos and alltracs are pretty rare.