Okay, this is how I would install the timer bays.
First, you don't need to cut the 29mm or 54mm tubes any shorter than they are. Secondly, I would recommend getting two more CR's. They should have holes for a central 54mm and two 38mm tubes on opposite sides. Then install the one CR just forward of where the 29mm motor mount tubes stop. Install the other at the very forward end of the 54mm tube. You should have 2 38mm tubes installed that are almost flush with the forwardmost CR but extend aftly through the other CR with the 2 38mm holes in it a couple inches. Bulkheads (with small holes for 1/4" copper piping) should be epoxied into the aft ends of the 38mm tubes. Then, run copper piping (two pieces) from the aft most centering up through the bulkheads in the 38mm tubes. These are the conduits. Then, you can install two ST-1 or Accufire timers into the 38mm tubes using PML's urethane holders. Secure the timers with a few bolts with mirror clips like you do for motor retention. Then, when you want to fly, just run the e-matches down the conduit, out the aft end, plug them into the motors and attach the other ends to the timers and screw down the timers.
Most of this needs to be done during construction, not afterward, but it is rather inexpensive except for the timers and urethane holders which can be purchased later. I'd say except for those things, it would cost about $35.
The good thing about this setup is that it is lightweight, it can airstart the motors in pairs or all 4 together and it means that there are no hatches on the side of the rocket so it doesn't distract from the finish.
Well, that was a mouthful. If you need a better description let me know, I can draw a quick little pic for ya.
David
PS- I don't do hybrid so I don't know.