I have owned both CJ's and YJ's. I owned a 47 Willys CJ-2A, a 1972 CJ-5, a 1980 CJ-5, a 1987 YJ, a 1995 YJ and currently working on my 1954 CJ-3B.
I like the both of them for different reasons. Parts, adapters, this & that are easy access for most from the WWII MB's to the last YJ. I will say that the short ones (CJ-5,3B,2a etc.) are limiting as far as drivetrain is concerned. Many do it but I don't like the short driveshafts needed for say to put an automatic transmission in my 3B. That's why you may want to stick with a CJ-7 if you think you may want to change drive trains. The early Jeeps, (Willys), have super low gearing so if you plan on driving it on the street, you'll have to change the axles out as selection for the 10 spline Dana 44, and 25 are limited. Mine won't and I'm a happy camper with low gears and lunch box lockers.
With all that said, I would, (if I were you), go for a YJ as they will be more abundant and a better bang for the 3K bucks you got. Also almost anything will adapt or fit should you later want to toss some heavy buckage at it.