If I may offer a cheap-ish idea to try?
Run a tank of premium fuel in the tank. Drive what you have until practically (best would be actually) empty and then fill it full of the high octane stuff. The idea is to get the gas feeding to the system as high an octane rating as possible.
Why? Often when installing a stroker crank and doing head work, the compression ratio is raised and the stock combustion chamber is designed to run on the low octane-rated stuff. From what you have said, to me it sounds like you are getting pre-detonation in the chamber, and when under a load, the pre-detonation is getting worse-typical of running too low a fuel rating with a higher compression motor. The On-board computer is designed to eliminate this condition by advancing or retarding the timing as well as adjusting the flow from the injectors. However, its designed to do this for a stock motor. All the extra cooling add-ons are helping, but are a band-aide to the central issue causing the overheating.
Adjusting the octane rating to meet the need of the specific engine is pretty common in racing applications where mixing different ratings of racing fuel are necessary to get the ideal octane rating of the fuel. NASCAR gets away with selling only one 'octane' rated racing fuel because it mandates the combustion chamber cc's as well as the max compression ratio the motor can run; ergo everyone needs the same octane rated racing fuel. Drag racers are not quite so bound by this handicap.

I used to run into this issue when I raced Air-cooled engines frequently and you'd be surprised at the amount of heat the wrong fuel rating for a given engine can create. Likewise, it'd run much cooler with the correctly rated fuel flowing through the system.
The easiest way to up your octane rating.....well, is to buy premium gas. If it doesn't work, you aren't out much (relatively speaking), but if it does....... The price one pays for having high-performance goodies,eh? :thumbup:
As a side note: do NOT use a bottle of octane boost to try the same thing. These products are NOT going to raise a tank of gas to 104 octane or whatever...all they do is inhibit the fuel's ingition, causing you to burn significantly less efficiently; which is why you added all these parts in the first palce-to run more efficiently