DO NOT PUT CLR IN YOUR COOLING SYSTEM! it will eat aluminum parts (like your radiator, for example).
if you have hot air out of the heater, your heater core is fine. there is a valve that stops flow to the core when the heat isn't in use anyway so a plugged heater core shouldn't cause overheating issues, although in a bind you can bring the temp down a bit by turning the heater up to max-heat. It's misserable driving but I've limped home a couple times in the middle of summer with the heater on high.
if the coolent is flowing ok, then you may have just coated the inside with bars-leak residue and it may be interfeering with heat transfer from the engine to the coolant. you said you used both prestone flush's, did you leave the long-term one in for the full 3-5 hours at operating temp? there is also a product called 'water wetter' (there are other brands too) that improves heat transfer to and from the coolant making the system more efficient.
it looks from your post that you changed out most changable parts on the water side of the cooling system. how about the air side? is your fan shroud in good shape? clutch-fan working properly? is your A/C 'radiator' clean, with all the cooling fins straight, and allowing air to pass freely through it and on to your radiator?