IME you can modify anything.  The issue with the non GT exhaust is that it might not have the pipes coming out in the right spot for the holes in the valance.  How much finageling it takes to get them to the right spot who can say.?  I used a Magnaflow kit for my '67 and modified a stock set of GT tips by cutting the pipe section off and marrying them to a length of stainless 2-1/2" pipe.  I used the ends off a JBA H-Pipe to mate to the Magnaflow X-pipe (collector compatibility).  Then I made adjustable mounts for  the tailpipes so I could get them in the right spot in the valance.  Took some doing, but the finished product looks awesome and only took me about a day. 

I would say start with a GT specific kit if one is available.  Exhaust on these cars is not like late models where it all just bolts on without any modifications.  You'll end up doing some modifying regardless of how good the kit is, but the closer the kit is to what you need the less time you'll spend. 

It depends on what your engine combination is, as well as any planned future changes.  For a modest small block under 350HP 2.25" is probably just fine.  If you plan engine changes in the future then I would size the exhaust based on that.  I run a 2.5" system because in the future when I'm running my 347 I'll need the bigger pipes.  Its overkill for my current 289 (sounds great though), but I will now be able to just drop the new engine in without worrying that the headers or exhaust are too small for it. 

Right now I have 2.5" from the exhaust manifolds straight back no crossover. then to some flow master 40s 2.5" dual out under the valance. Really do like the aggressive sound it has now. I just want to change my tail pipes so they exit through my GT Valance.

I managed to hit the cutouts in my GT valance just fine with 2.5" pipes.  You have some latitude as to where the pipes come out by clocking the tailpipes relative to the mufflers.  This is why you never tighten anything until you are fully mocked up.  Use jack stands, blocks of wood, cinder blocks, whatever to temporarily support the mufflers and pipes where you want them.  That way, once you start securing the system with hangers there's a lot less guess work and frustration. 

MS wrote:

My 2.5” JBA stainless tailpipes are designed for valance exit tip and fit perfectly. On my 66.

 
How do you like the fit up on the JBA kit in your car?

I have a 302in my 66  that runs fine has good power but has a minor miss on the driver side. I have changed the carb gasket and bought a new carb ,and still have the same issue . engine starts to tremble around 2500 RPM . can someone please help me .
I changed the plugs and the ones on the passenger side was golden brown .The plugs on the driver side was black .