So you introduced air (had heat, then removed hose) into cores, than filled radiator again.
You must also do the 8 hour cool down and top again. It's the heater cores that are most difficult to get air out of. Since the engine coolant level must be full, to get coolant to cores. Than it enters cores and push air back into engine, and we're low in engine again. Topping (getting air out) can take a few days of heating and cooling cycles. When topping you must fill radiator and reservoir.
Also make sure you've a good working radiator cap (new Toy OEM) and no restriction in reservoir hose/cap (i've seen these clogged) all the way to radiator.
Also make sure reservoir hose is straight and drops to bottom of reservoir. I see many, where reservoir hose gets caught on inner shelf and curls upward. The reservoir hose then sucks air back in radiator, even when reservoir appears to have adequate coolant reserve level.
If any air in radiator, the reservoir and radiator cap no longer work properly. The radiator ends up low.
Note: Do not remove rad cap during the 8 hour cool down. Doing so introduces air and system loses vacuum created by cooling. It this vacuum, that draws coolant back into system.
If you're sure; no air in system, reservoir & rad cap working as they should and cabin heaters works. Then after cooling and bring engine back up to op temp again and cabin heaters stops working and air back in system and engine overheats:
You've blockage on engine side, if no air found back in the system. Which since issue began after bypasses off and rags used to block ports, is high on list of possibilities.
Or
System low again, so you've an internal leak. Like head gasket. Which could have happen from overheating after your starter/bypass joint gaskets service.
BTW:
Radiator hoses that collapse during cool down, are past useful life.
Tip: You could use a clear hose to bypass heater cores. Run hose from engine out (rear water bypass pipe on driver side), to inlet (water crossover pipe passenger side). You'd then be able to watch flow of coolant and or air. You'd also eliminate cores as any possible issue.
If you'd like to talk on the phone. Post you phone number in the PM you started, I call first chance I get!