I'll try and answer some of your questions as quick as I can...
Questions 1 & 2 go together... I replacement ECU is the best way to go and allows you to eliminate the MAF by running a MAP (Manifold Air Pressure) sensor. It allows more flexibility in tuning and perhaps running other devices (water injection, boost control, etc.)
Stock TB can be used, but the shape makes it tough to plumb the system. I think it's restrictive as well.
If you can weld really well and have the tools you can fab up a manifold, but there is a fair amount of science and work in creating an equal runner length (tuned) manifold. A log is easier but much less effecient, especially with a 4 cylinder.
I'm not sure you can get enough displacement in an M42 to justify a T4 turbo.
Tubing size depends on a number of variables as well as which part of the system you're talking about. Pick up "Maximum Boost" by Corky Bell for info on manifold, intercooler, and exhaust plumbing.
Can't comment on the Evo turbo as I don't know what it is or how big.
Now that I answered your questions, here is an off the top of my head list of the decisions you'll need to make for a full turbo build. For some you can say "Keep it stock" but you still need an idea of what you just decided.
Stroke, bore, compression ratio, CAM lift & duration, valve size & spring type, rev limit, spark plugs, injector size & type, fuel pressure, fuel flow (pump), ECU, intercooler size, intake plumbing, throttle body size, oil cooler & plumbing, radiator size, exhaust manifold type, material and tubing size, exhaust pipe diameter and routing, BOV & waste gate springs, O2 sensor, instrumentation, waste gate/boost control, internal/external waste gate, turbo flange, exhaust flange, turbo size, trim, and A/R, oil return to block/pan, clutch and flywheel. PLUS all the mounting, plumbing, and routing decisions to make it all fit and work.
Then you have to find the parts and put it all together.