The following is the best of my knowledge, from speaking with former GasGas tech help people, and from speaking with dealers who tried different experiments. The last set of bike cases which easily take the counterbalancer shaft are the "true" '99 model bikes. In 2000, or 2001, the cases were slightly modified for strength, which put some of the castings in the way of a simple "line sight bore" to get the shaft and bearings in proper alignment.
In the "true" '99 engine, the opening in the cases is large enough to accept the 300cc cylinder without modification. I think that the holes for the c/b shaft will have to be bored in that model cases. It's either that, or if the holes are there, one needs to have the cases machined (line sight bored) to to make sure the holes and bearings are properly aligned.
In the '96 model through the '99 Prototype (early model) 250s, all were predrilled to accept the c/b shaft, with the motocrossers (without the c/b shaft) having a metal plug inserted in the ignition side to keep the oil from getting through to the ignition. These cases will have to be slightly trimmed to accept your slightly larger 300cc cylinder skirt.
The 300cc quad engine is essentially a "true" '99 300cc engine, with the cases bored to accept the c/b shaft. It even has the larger magnesium ignition cover that the '96-'98 came with (to allow the extra lighting capacity). If you go this way, get an early model 300cc quad engine, without the reverse.
In 2005, they changed the cases so that the hump in the cases where the counterbalancer weight spun is no longer full size, but only large enough to allow the pick-up coil to be installed there when the larger EC ignition is used.
Even though the 2000 through 2004 cases have the full sized round "hump", the cases are not conducive for installing the countebalancer easily.
With the counterbalancer installed, one will need to run the smaller flywheel mx ignition, because of the need to mount the pick-up coil at the "8 o'clock position, since the counterbalancer weight is taking up the space in the hump. (If you desire more lighting capacity, the magnesium ignition cover will allow you to run the original Ducatti style lighting system.)
I believe all of these engines will mount in any of the 200cc to 300cc bike frames, of any year. One thing, though: The water intake casting on the '96-'98 engines is very tall, and will have to be machined down lower to match the height of the '99 and later engines, in order for there to be enough room for it to fit under the fuel tank.
Also, the counterbalancer shaft will act a bit like an extra flywheel weight. Not a big difference, but it will make a difference.
I hope that this helped you. If you do install the counterbalancer, you will be amazed at how much smoother the engine runs, especially at higher rpms. I really liked it, and rode my '99 prototype (which came with a '98 engine) as my primary bike for almost six years.
I don't have any experience with 2007 or later bikes, but definitely prefer the 2005 and later chassis to the earlier models, except for the 1998 chassis. I really like the 1998 chassis with the 2004 and later Marrazocchi 45mm or 50mm Shiver forks. (The 1998 chassis was different from the earler models, and turned much better and was more stable than the '99-'01, and turned better than the 2002-2004 chassis.
I really liked the changes that were made to the 2005 chassis, and the look of the black powercoated but otherwise identical 2006 chassis. I absolutely love my 2006 300. It's the best bike that I've ever owned.