700R4 vs 4L60E behind a V8 swap in a YJ - which 4-speed automatic is better?

They're the same basic transmission: the 700R4 was renamed 4L60 and then became the electronically controlled 4L60E (trucks from 1993). Internally they're mostly the same; the difference is control.

• 700R4 / 4L60: hydraulic control. Simpler with a carbureted engine — no computer needed.
• 4L60E: shift timing and line pressure come from the computer. Far more tuning flexibility, and the natural choice with an LS or other EFI engine.

Either way it's a light- to moderate-duty transmission. Heat, weight, big tires and towing shorten its life, so plan a big external cooler, and build it (3–4 clutch pack, input shaft, sun shell) if the Jeep will see hard use.