Your best bet is to find a donor jeep with a good drive-train. A junk yard will be quite expensive for everything you'll need. The 4.0L tends to get a little better gas mileage because it is injected. The 4.2L and the 4.0L also have different pilot bearing sizes, you can purchase a new pilot bushing to mate a newer tranny to an older motor, should you decide to use parts from multiple years. Stay away from the BA-10 (Peugeot) transmission found in '88 YJs, they are horrible. Early AX-15s, from '89-'91 or '92, have a weaker reverse gear than '93 and newer. If you can find a complete jeep with a bad frame/tub or a wreck than runs, you wont nickel and dime yourself to death. Two summers ago I bought a jeep with a bad motor then bought two more parts jeeps and was able to sell the spare parts and almost completely pay for all three. You may also want to check out a jeep forum, chances are someone near you has something you can use for pretty cheap.