Being there, doing that.

http://forums.swedespeed.com/showthread.php?201780-What!-Another-142-Project-Car/page2

Doing a good MS implementation on a B20E is not super difficult; but, there are a lot of details and a lot of misinformation out there. The Djet was a pretty good system and runs nicely when everything is working. Its biggest operational problem is bad connections and wearing parts (after 40+ years). The biggest future problem will be replacement sensors, particularly the TPS, idle air valve, and the MAP sensor. MS has the advantage that it can be fiddled to make just about any sensor work, so it has some future survivability. Being able to plug the laptop into MS is nice because it will give you clues if something is not working.

Unless your Djet turns out to be a big problem, I would not rush out to replace it with MS (unless you are looking for a new project after you fix your heat soak problem).

Rather than switch out fuel pumps, borrow a fuel pressure gauge. I hook mine up to the tap for the cold start injector. Connecting a pressure gauge is much easier than groveling around under the car dropping and re installing fuel pumps (lord I have done enough of that!). It will also confirm that your base running fuel pressure is correct which can also mess up your starting if it is off.