The impossible to solve overheating problem

Hello. Read through this thread twice and while there have been a number of great suggestions, I thought a little different approach may help. Keeping in mind this is not a criticism towards you or any other members posts, a Flow Chart/ Diagnostic Tree mindset may get you closer to resolving this problem. Please forgive the length of this post as it may get a little wordy.

First, in the 5th paragraph of your original post you said, "The car came with the original cooling system (4 yrs ago now) and would overheat once in a blue moon I don't know why "......STOP......

This tells us there's been an intermittent overheating problem from the start and brings up some questions:
A) What's your definition of "once in a blue moon "? For instance, if you only drove the car once or twice a month for 4 months a yr and it overheated 2 or 3 times in that period, that could mean a problem 25% of the time, or possibly more. This could be significant.
B) You then said, "I upgraded the cooling system (2 yrs ago) and it never overheated, well, it did a few times but I had the timing too lean".....STOP.....This tells us there was STILL a problem after the upgrade. Setting aside the "timing too lean" part, this is important because in the next paragraph you talk about the car sitting for 2 years after pulling the engine. If you did the upgrade 2 yrs ago and pulled the engine 2 yrs ago, did you drive the car enough between those two events to really diagnose whether or not the original problem was solved ?
C) In the second paragraph you give a description of the engine. Is this the EXACT engine you started with from the previous owner? Was it upgraded over the first 2 yrs? Or aside from the 3 changes you listed in paragraph 6, were the upgrades done after the engine was pulled?
D) In paragraph 6 the problem,( after the engine R&R and sitting 2 yrs) became in your words, "massive". Other than the 3 things listed, were any other changes made to the engine/cooling system?
This is just a starting point depending on your answers to the above questions. Be HONEST w/ yourself when answering. Using the Flow Chart mindset, you may need to backup, flip on your memory banks, and see the car as it was ORIGINALLY. Then, identify which parts/conditions are still part of the systems and look at those FIRST. If you don't use a systematic approach to diagnosing the problem....you're GUESSING, and the more you change, the more difficult finding the underlying problem becomes. Diagnosing "with the Force", in most cases, will do nothing but increase your frustration/aggravation level and lighten your wallet.
I know I haven't given you any specific answers, but hopefully this will start you down a different avenue because the one you're on now doesn't seem to be working. Good luck and chin up, you'll figure it out. Cheers

P.S. On a personal note, sooner than later, you need to take the car to someone who has a professional coolant flush unit and get that crap completely out of the ENTIRE system if it hasn't plugged up part of the engine/radiator/heater core already. Just sayin.