Here are some additional differences I didn't see mentioned above....
1979 Z50's had actual bar clamps. The bars can be tilted forward and backwards, which cannot be done on the other Z50R's because the "bar mounts" are tack welded onto the bars so it is fixed in place at a specific angle. If you don't keep the stock bars on a z50r (besides the '79) , you can replace them with with 7/8 bar mounts, or find something that works. I did this on my 83 Z50 to give me the ability to run the Pro Taper Mini Racer Bars without spending the money on the bar mount kits. I believe the bar mounts I used were off of an XL70, snagged em on ebay for about 15 bucks and they polished up really nicely.
As Dirtbkr188 told me,
The bars on the '79-'99 Z50R models are 7/8". The bar clamps used on the '79 are also used on the XR/CRF70 models from '97-'12, as seen here.
Another thing is the '79 did not have a number plate on the (right) exhaust side. I modded my 83 instead of my 79 for that reason specifically....I wanted to use number plates on both sides and that was important enough to me to be what led me to my decision. Not a hard thing to add, and you may be replacing the exhaust anyways, but that's just a minor little difference that actually did influence me in my decision sense my 79 and 83 were both in similar condition.
Like mentioned, different colors etc....Only real differences were decals, rim color, # plate and fender colors, and frame was white instead of red in 87. You can always find aftermarket seats, repop seats, or seat covers, plastic fenders in various colors, repro tanks, and so on...not a huge deal.
If you really do end up going crazy modding it, and you have motor mods/aftermarket motor, aftermarket forks, extended swingarm, rims, etc....The only thing that will matter at that point is the frame honestly! Haha! If you aren't planning on repainting the tank or frame, they did switch from Tahitian Red to Blaze Red in '82...(big whoop

) And like mentioned previously, The frames and motors will pretty much all go together besides the short rod and long rod stuff. In the long run that's not too important, you can easily find parts for both motors. Sky is the limit on craziness, I'm doing a totally custom CT70 build at the moment with frame mods, and all sorts of craziness that has never been done before (that I know of....and if it has, I guess I'm not the only idiot in this world!!

) I've already invested over a grand into the frame, and motor. Not hard to have fun and get "a bit carried away" as my friends might say.
My advice is to try to go into it with a plan. I used to spend countless hours just looking through EVERY SINGLE PICTURE in the z50 or ct70 pictures threads. It'll give you a lot of ideas, you'll see parts you thought you wanted on someones bike and decide against it and see how bikes look with different suspension, wheel and swingarm set ups that you may like or want, etc. If you have a general idea of what you want, it'll make it much easier. You will change your mind many times along the way I'm sure, but at least having some sort of direction helps a lot.
I like to make an Excel spreadsheet and total up my investment in parts including shipping to know exactly what I have in each bike. (Custom build or not) That way if you do have a budget, it's harder to get carried away and if/when you decide to sell it, you have a better idea of what to ask or at least know what you have in it. I will say, after you pour your heart and soul into reviving a mini and making it customized to your own liking....you won't want to sell it. It's addicting...BRB, gotta go pick up another z50. I've been needing to take another hit.
Aaron