During the AMC years, Jeep allowed every possible gear ratio to be ordered with any package. But 3.07 was the standard ratio with the 4.0l and manual transmission. The 4-cyl's got a 4.10 standard.

I understand that, but it was my understanding that with the tow package had lower gears.. regardless of auto or manual

I would recommend manual trannies, it's nice being able to directly control your speed/gear ratio. This is really nice for engine braking. I have this thing about automatic features on cars. Other than abs....I like having everything be manual (I don't even have abs on my XJ). Even if it isn't as "efficient" or "easy" to do things in a stick, it's nice having that extra level of control sometimes.