I dont have any experience with this swap personaly. The info I put up is what I found doing a google search because I had heard it was not a straight forward swap. The problem I see with this swap is you have a cj and are putting in a yj engine, trans. The cj never came with the trans or tcase that the wrangler uses, and the output shafts of the wrangler tcase is on the wrong side, so you cant use it, and you will probably need a adapter for your current 300 tcase to bolt to the wrangler trany, the adapter kit will probably have a new mainshaft that will need changed on the trany. It would be simpler it find a cj engine and trans for your swap. The reason is you will not have as many complications. If you use the wrangler engine there is computers, tcase adapters, probably wiring harnesses because your new engine will be computer controled and the cj is not. If you get a cj 258 and trans the only major things to change will be motor mounts and moving the crossmember back, and the driveshafts. you will be able to use your current tcase without an adapter which will save big bucks.
If there are no hole, You may have to drill new holes in the frame for the crossmember either way you go, but thats not a biggie. I would change the water and oil pump before intalling the new engine. For the driveshafts, if you have a 4x4 shop close by, check with them to see if they have used 6cyl driveshafts and give them the measurements from the tcase yoke to the rearend yoke. Thats where I have gotten mine in the past.