sad part is, even if you get a 304 in the CJ, at it's best year it only put out about 150hp and got even more dismal as the years went on ending up at about 125 hp in the early 80's, while the 4.0 HO found in 91-95 Yj's is around 180 hp. Even non HO motors were around 160hp. Both engines get around the same torque numbers, between 220-240 depending on the year. so weight to power ratio would be better for the I6 in this instance.
A Yj with MPI will be far more reliable as a driver. both will have the same durability, but no carb to rebuild. you will get way better milage with the YJ simply because it has an Over drive transmission. depending on the type of wheeling you do, the 2.5" springs in the front of the YJ will be a bit more durable than the 2" ones in the CJ, again, depends on the level of wheeling you do. in the instance here, I think it is not a issue.
The galvinized body is a huge plus, especially when you have a budget and buying a bunch of repair pannels is just not needed, and in most states(like massachusetts) a vehicle with rusted body pannels will not pass inspection and will not be allowed on the road, so rust is a issue here.
round head lights, square head lights.. Honeslty, who really gives a fish hook, as long as they work.
all in all, do what you want, have fun doing it.