Of course pipe length affects thrust. The wall friction slows down the airstream drastically, so the longer the pipe the more you loose along the way. With a good pipe design, this can be minimized. I use pipes with a golfball surface to create a turbulent boundary layer and reduce the overall loss. Works excellent, it is just really noisy (My MW puts out quite a lot more sound than any 160 class i've seen).
The optimum solution is to mount the turbine directly in the airplanes nozzle. That way you have set your fire hazard down to almost zero (if it burns it will simply burn behind the airplane), plus you will get true turbine thrust. I'm doing that in my Avonds F-15. Batterys all up in the radome and CG should come out all right.

As to the gap between thrust tube and engine: there is no "rule of thumb". How far is drastically affected by turbine mass flow, nozzle design and exhaust gas characteristics......in simple words: it varies from turbine to turbine. Best way is to build a test stand on which you can adjust the gap with a screw. Run up your turbine, and turn the screw until your thrust scale peaks, that way you will get optimum (static) performance from your turbine.
Also, have the thrust tube end before the airplane nozzle ends. Depending on the "space" around the thrust tube about 1/2" to 1". That way you will get a venturi to suck the hot air around the pipe out of the plane when sitting on the ground, plus static thrust is also increased slightly.

Regards
Hank