where to start? lol learning about the car before buying one is a step in the right direction. however i doubt your gonna like my advice, but this is just my opinion. The mr2 is not a beginners vehicle and I really suggest against this as your beginners car. plus the numbers you mentioned dont really line up.
one: you should check out the above thread on engine swaps, but the 4-5 grand price cap you can pick up a mk1, or a n/a mk2. the turbo mk2 usually runs 5k+ and emphasis on the + for a good one. though there are deals out there. dont get me wrong. opinions? i think the mk2 looks supurb, nothing beats it cept maybe a skyline hahaha. but depending on your goals for the car, drag, autocross, hill climbs the diff engine and stuff i guess could have some bearing on your choice.
two:again, engine swaps can be COSTLY especially if this is your only means of transportation. unless you can do all the work yourself or line up some good deals on everything, expect to be shelling out five large to swap an n/a to a turbo. better off getting a turbo that needs some tlc for 4500-5500 and do a rebuild or something.
three: depends on mk1 or mk2, and if your going n/a the 2.2 5s-fe is a peppy motor and the car wil still be lots of fun. specially if you dont know what your missing from driving a turbo. the 5s "has" potential, if you properly build it, though to match a 3s in potential, the 5s will cost considerably more. but some good short term gains can be seen with bolt on turbo. wich is more than enough power for street use.
four: body kits are at your discression, its your car and your money so get what you think looks best. however, some ideas pros' or cons' such as part quality for price just ask if anyone has they can tell you their personal experiance.
five: not really sure what your asking for, are you talking about brakes? suspension? transmission? if you start with a turbo mk2, the engine and transmission are good for most your needs less your are going all out and then some.
so i guess, keep learning about the mr2, and decide your goals, and see if it fits. if it does, we welcome you to the mr2 community

they are amazing machines and need to be given the respect they deserve. out of production means, wrapping one around a tree is one less for the world to enjoy

lol