I took your advice and checked the VAB and this is what it said:
https://imgur.com/a/KTWSJhj
After I found this to be ok I added a load more radiators and tested again, its like the system isn't even interacting, as if the nuclear engine is not dissipating heat using the loops. I got this ship to work once, immediately after I had docked them together it seemed to work, but now whenever I load this save up I am having this issue. Also if its any help whenever I have this issue, the reactor starts to churn out a load of heat and there is nothing in the heat ui monitor saying that there is any rejected, then all at once as soon as it hits max threshold and the reactor scrams it all appears in the rejected all at once, like 2.5k rejected and then falls off, but this might be a feature, I don't know this mod to well
Oh and thank you for the wiki link