I might be wrong but I believe port diameter is different on the GSXR based engines and everything but the '83 and up 700/750E models. I had picked up a GS1100 V&H pipe but the pipe diameter was too large for my ports. Does the GSXR based pipes have slop inside the port? The GSXR based stuff is the same as my 700.
Billy,
The simple answer is that the port sizes must be close enough (maybe no more than 2-3 mm diameter difference).
My Yoshi 2nd Gen GSXR1100 4:2:1 fits nicely inside the GS1100E as did my Muzzy 4:1 from 1st Gen GSXR1100G (86).
As mentioned it is the flange bolt hole spacing that is smaller on the GSXR with the required modification of replacement of the flanges. Tone's B12 flanges were slotted (as mine were done in that picture) so the pipe can go back and forth between GS and GSXR.
From the measurements on both my 2nd gen 4:2:1 pipe as well as the 1st gen 4:1 pipe if you get the flanges properly configured so that the pipe can bolt up without intereference with the frame, the depth under the belly is not excessive and should work well. The GSXR750 motors have a shorter stroke and probably would not fit the GS1100.
Jim