man, just build a whole new m50 engine! its an easy swap (drop in and go, almost) and you wont have any down time. plus, you can rebuild your original engine and ebay it to balance extra costs on the m50!
Thats what i will be doing throughout next year. i can give you tips on the m50/52 engine, but dont care to learn much more about the m20, so im no help if you are stuck on what you mentioned.
i originally though about rebuilding my engine, but found out it would be highly beneficial to change. of course you lose the authenticity of your old car, but sounds like you were planning on that with the stroker kit anyway.