OK. Firstly hats off on envisioning such an ambitious project. After my recent Dubai visit, I confidently believe that its a worthy cause to undertake this conversion, provided (a) one has the finances and jigra (b) the Wrangler parts are in good shape (c) you have expert conversion masters at hand for body and mechanical work. Now, as for some of your immediate questions:
I beleive that all CJ 7 chasis are pretty much the same. The later models (1983ish to 1986) had wide track axles while earlier ones had narrower ones by around 3-4 inches. Both however had the same chasis from what I understand.
To the best of my knowledge the CJ7 and 2000 TJ Wrangler (plus the earlier YJ with square lights) have approximately the same body dimensions.....
The CJ7 wheelbase (93.3 inches) was pretty much continued as is until the new JK model in 2007. The 2000 TJ has a 93.4 inches wheelbase so there should not be any major issues here in terms of where the diffs would sit vis a vis the chasis. The body width is also pretty much the same for both CJ7 and TJ. The height of the two is different but I don't see that as a major issue.
Hence, though there are many minor body variations, the only tricky one appears to be that the TJ has a 6 inch longer body, though I am not sure how (or from where) if the wheelbase is the same and it may just be a measurement difference....needs some more research!
Regardless of the above, fitting a TJ onto a CJ chasis is no small affair if the project is to be worth its weight. From what I understand, the chasis are similar, but they are by no means identical. Body mounts will require special attention and the fittings would need to be perfect not to give the whole thing away. Not a small understaking by any means.
The most interesting and tricky part will be mounting the coil spring suspension onto the CJ7 chasis. Its been done pretty successfully in Rawalpindi (Prado coil suspension on CJ7) but its a lot of work and khwaari to produce the right result and pretty easy to mess it all up here...
Bare CJ7 chasis are difficult to find these days but should not be more than PKR 100k or so with papers. Probably easier to find a fullish wrecked CJ7 in Shershah Karachi or maybe Bilal Gunj Lahore....
Lastly, all said and done there will be those that will argue that one can get an original Wrangler in the cost of doing such a project and be spared all the khwaari. The argument does hold merit if one can get the right deal on any Wrangler in decent shape, but quite frankly there would be many more Wranglers around if such deals were readily available.
Anyways, hope that helps....and best of luck!