Yup, thats the main reason I have tried to keep up my build website, so everyone can share in my experiences.
The back frame I did move up about 2". I did it with 2 1x2's welded together with part of one of the 1x2 offset a little higher to really make sure I had room for the mufflers. Pictures will really show what I did (which are not up on my build site yet, but should be soon).
I also had to make some additional frame modifications due to a problem with my seats.
Up until now I have tried to make sure and get a sample part for fit, to make sure everything would go together. A good example of this was my rims and wheels. Before I dropped a bunch of money on the wrong size rims, I had the place I was getting the rims from send me one to test fit.
When it came to seats, I shopped around a bit, and then decided to get Cerillo's. The place I got them from only had one seat in the shop and did not want to loan it to me to make sure it would fit, but guaranteed me they would fit in a bug no problem. So I took there word for it and orderd 2 seats, with heat, custom covered in the same red vinyl as my dash and door covers. 3 weeks later the seats show up, and they look awsome and feel great. I get them home and plop them into the tub...and they are too wide, by about 2". AHHHHHGGGGGRRSFFDSFKJL.
After stewing on the problem for a little while I decided I could get them to fit if I cut out a long notch in the 2x4 steel frame that went under the doors. I'm about half way through this modification, and again will post pictures and a full writeup. But for anyone else out there modifying their kit and going outside the "normal", MAKE SURE to get example parts or components to make sure things fit before you drop a bunch of money. In my case the seats were just over $1k each. Well worth the cost in the end for the comfort (and heat), but a little bit of stress when some major mods are needed to make them fit.