Now that the big parts are all mounted, and there is still room to work, the RF cables can be assembled, routed, and connected to the correct places.
Avoid using RG-213 here, as it will not hold up very well at these power levels. LMR-400 is the better choice; it can handle the power, is flexible enough, and has half the loss.
2 of the cables (in and out) are fitted with a male N connector on one end, and a female on the other. These are routed top and bottom, respectively, to keep cross-coupling to a minimum. The output cable is bent to allow an inch clearance from the water jacket on the tube (there will be 2kv there).
2 others (cavity to relays) are male-to-male.
The bypass jumper is 1/4" semi-rigid with a male connector on each end (LMR400 can't quite make the bend in this space). You can use UT-141 or RG-213 here if you like, as the power level is low and the jumper is very short, so loss is not really an issue. I only used the 1/4" stuff because I had it, not because it was necessary.