there is a lot of questions in there, you would be better off just getting a turbo mr2. If you are still going to do a swap, I personally have and it was a long drawn out nightmare. Your going to need to make sure you get everything with your swap. Im talking engine, ecu, harness, new fuel pump, clutch, transmission, rear axles(you will need both sides of the rear axle either machined ones to fit the turbo tranny and the NA wheel hubs, or need to swap the wheel hubs/wheels, not exactly sure as I got machined ones from an MR2 vendor), exhaust system, intercooler, some kind of intake(even if its just a filter and hose from auto zone), and this is assuming everything else on your car is in good working order. most notably your cooling system. Im sure im even forgetting stuff but like I said, just buy a turbo mr2 if that is your end goal.
About repinning your ecu, I dont think I understand what you are asking. If you would like I can take a picture of mine in the trunk. Everything was wired using pin and wire diagrams, and spliced. I dont know how it works, I just know the shop eventually got it going and there are like half the wires just capped off not connected to anything. And thats using the jdm ecu and harness. and just so you know, an uncut one still comes cut off on the wires that connect to the chasis.
about power, I suggest reading the power primer
http://www.mrcontrols.com/primers/power.htm
its not as easy as just turning up the boost... and the mr2 3s is a very easy engine to get more power out of. The 3s-gte 2nd gen with the ct26 and its fuel system will fall short of your goal. gen3 should be able to hit that with its larger injectors and ct20b, but when you push things, things start breaking unless all maintenance and other supporting mods are working properly.
bottom line, do a lil more research before undertaking this project.
suggested threads to check out, search for anyone who did swaps. mine was
turbo swap
and the power primer. everyone goal is different, and the purpose also changes what power you want. auto cross. drag. track. drift. also look into people who have already gone the path that you want and ask them questions as well.
http://www.mrcontrols.com/primers/power.htm