Jjet, Not sure I understand your problem. Is the tail pipe out of the tail cone or inside of it. If it is inside just move it back and move the engine back to keep the spacing.
If the tail pipe is too far out you will need to make new rails for the engine mount. In post 124 of this thread you can see that my 2 front engine mounts are in front of the former on the rails. My pipe also is a very tight fit to the tail cone. This is why I cut the cooling vents into the bottom of the fuse. Also in post 124.
Hope this helps.