I have a Paul Turner "race" series pipe and a FMF gold pipe for my 87' trx250r. I cannot get the lower bolt hole to line up to anything on either pipe. The silencer looks good but I cant figure out how to mount the head pipe. It looks as if the pipe would bolt to the right side motor mount but it is about 3" from the bolt. Is there a difference in frames and these pipes are year specific? I was given both pipes from guys with 88'-89' R's. I am puzzled. This is my first R though so I am pretty green.

 

There are some differences in front motor mounts from year to year on the Rs. You may just have to get inventive and fab a mount. Happens all the time. I have home fabbed mounts on my 86. Just don't do anything half-assed and you'll be happy with it.
Just get some longer bolts, and a short piece of pipe that can be used as a spacer. If the holes line-up like you said, this should work.