Maybe I'm missing something but it seems like power is supposed to be installed on the bottom level due to the heat exchanger upgrade being based there...but it doesn't seem to be transferring all the power up to the top level currently. Hope i'm missing something here but any information on it would be appreciated.

Or I guess the main problem is I can't charge the warp stabilizer or warp gate from power generated in the lower levels. Possibly due to how they are all considered accumulators?

I came to the same problem.
There will be exactly tranfered the power needed by the factory on top.
The warp stabilizer is not taking into account.
Thested these with the power supplyer from cretive mod.

Also wired to me is how to power the heat exchanger. the reactor wont eat up the fuel cells.