I built 3 setup to guide and try to trap the particles, that seem to do their job well, but even when 5 particles get trapped and go over rows and rows of chests the conversion rate seems super low, are there other factors that affect it ? like how much u238 is in the chest, or if u235 is present, or chest density lowering chances or something

with the cooling rate of the reactor I just can't get enough plutonium to sustain it

There is a Tips&Tricks entry that addresses this, unlocked during the Cerys tech tree.

I see Cerys Briefing but nothing else besides that, at what point is it supposed to get added ?

Quite late, it's unlocked at Plutonium Weaponry.

Ah, I was hoping to get the reactor running before going that far since it's a 500 pack research, fair enough though, I'll let that run for a while and see what I'm missing