On my F-22 thrust line I basically "eyeballed" it using highly sophisticated seat of the pants TLAR (that looks about right) technology. So far its been "about right". On the F-4 I used TLAR to align the the panel line on the side of the fuse with a carbon rod from the old fan mount out the center of the twin nozzles. Once again, it was about right.
If I could, I would put the fuel on the CG as much as possible. If for other reasons, cost, effort, parts on hand, time, etc you want to put the fuel ahead of the CG I would use the technique of balancing the model at landing fuel. For me thats 25-30% remaining. Then your not so nose heavy on TO and during the first part of the flight. I have found most of the "book" CGs are very nose heavy. I usually start a little farther aft and fly. Then I adjust it from there to my comfort and preference.
On my 8S F-22 I was flying around with about 4 oz of lead on the tail. See my post #15 in this thread. Was the same for the F-4. So I just checked it on my Xicoy CG machine and used that as a target for the turbine conversion.
The bottom line for me is the weight has not been that big of a deal. I may have been able to save a couple of oz by using a pipe and ultra light everything but it really didn't matter. I mounted the turbine in the tail, battery in the nose plus some extra weight, CTU, airspeed module, later added JP brakes, and they all flew great. Just wasn't a big deal. So my advice is to just put your stuff in there and fly it. It's a blast. Just watch the speed as you can get going real fast, real fast. No need for a foam explosion.
Just my two cents worth.
Gary