Change one thing at a time. Before you put on the upper & lower manifold, you said it ran. I would restore everything the way you had it, except the manifold. Then, start chasing your issue. You're running the risk of creating a multi-variable problem and confounding your diagnosis.
Great advice. Simplify a complex system to the base components that should work together, i.e. as close to stock / OEM as you can get.
I am noob here, but just went through a similar deal with the 5.0 in my 1967 Cougar over the past month or so. When she idled it was either high, hesitation off idle, very slow dashpot return holding high idle, or like it had a B cam. So many "missed it by that much".
Long story short, 02 sensor readings were very helpful once I confirmed they were real - "how can she be that lean and still have some wet plugs !?!? And why no O2 computer codes??" But after a 30-year IT career, I don't admit defeat readily. There is a reason, I just don't know it yet.
Returning all but the GT-40 to stock (removing Accel dist / injectors,
BBK TB) and then troubleshooting led me to: breaks in EFI harness, leaking FPR, worn OEM injector seals.
Car is running well with re-capped stock A9P, stock dist, stock TB, stock injectors and GT-40. Well enough to go downtown on date night with my bride
If I could buy only one of the many tools I now have (Quarterhorse, 02 simulator, among them) it would be the EEC-IV breakout box. It was invaluable. Mine is an OTC 3225. Prices vary on ebay, as does quality. Jakemart has one they are asking $225 for. Make them an offer. Search for "jakemart 3225-12508". If you need a manual, message here, and I'll scan mine. It's pretty simple but the manual does have a pin map and expected values at KOEO, KOER includes ID'ing all the grounds. It installs inline to the ECU and can be left in place while operating the car.
EDIT: There is the Thexton flavor of the EEC-IV Breakout Box on ebay now at $65 bid with a day or two left. Search "THEXTON 126 FORD EEC IV".