Yes you can move it to a primary tube, but remember,
you cannot use any of your prior results for data
1 - You had the TPS adjusted wrong
2 - You fired it a bunch of times and it got hot enough to enter learning with the TPS wrong and changes in fuel pressure
3 - You overheated it giving it bad data
4 - You ran it with low voltage a bunch of times
Again, ignore your old data and just get it running first and staying cool, trust me. This O2 sensor discussion is like chasing windmills until you can get it running and staying at normal temps, please please please....try to avoid helping or being helped until you have that squared away. Trust me
I also think the headers are no issue whatsoever, or better said, not a significant issue.
For the thermostat, why can't you just use a stock style for the cammer and add an inline radiator cap to the upper hose and use a solid lower hose? Seems like an easier fix, then use the degas bottle as an overflow if you want to keep it
ON EDIT, I think I figured it out..... I think your Saleen part is for reverse flow, there is no way it would get hot water to open the thermostat and the picture you have above seems to show the lower degas manifold without a thermostat. I think that maybe the diagram is for a standard flow, but your car was reverse flow.
You may be able to use the Saleen manifold
without a thermostat (leave it wide open) and add a thermostat to the SOHC water neck up top. Then it would match the diagram above
Note that I am not talking about fuel mixture just cooling.... and yes I am using my Colonel's voice with with all my bold LOL. I am the EFI lover in the room, but you HAVE to take one bite of that elephant.
Matter of fact, I think your visit from the header guy has the potential to cause more trouble if you havent got the cooling worked out. I'd wave him off if it was mine, at least until the cooling is fixed