ORIGINAL: rhklenke
Bill,
In addition to centering the engine in the opening of the pipe, you also need to make sure that the engine is aligned with the pipe. An engine that is centered in the pipe, but misaligned with the direction of the pipe can cause uneven heating and hot spots as well. Its not super critical, but a difference of more than a couple of degrees should probably be corrected.
At the aft end of the pipe, most jets have a former that has notches cut in it to let the ram air out of the aircraft. That is, in my mind, simpler, and more common that the standoffs that Danno made, but his method seems to work well and his picture looks great - even the jet... 
It sounds like Danno has a lot of experience with that aircraft. I know that there are (or have been) issues with that airplane with turbine power with respect to the formers, wing mounting, etc. being strong enough. It would probably be worth having someone like him look at the ''innards'' of your plane to be sure that its going to be strong enough...
Bob
Although Danno's method is more free flowing (less drag), what Bob mentioned looks like this and is probably the norm. Also, in regards to what Bob said in his first statement.. if careful use is imposed with the jig I showed, you will achieve not only centering, but also alignment of the turbine to the pipe. You just need to make sure the disk that fits in the pipe is square in the pipe.