Go 9". As far as the driveshaft goes, switch the yoke to a short one and it's a bolt in. My 9 " is from a Torino so I had custom wheels made. I used Cragar SSs and had a 12" wide rim made with 8" BS. This may not work for you as my Comet is tubbed.
I've pretty much made my decision to go with an 8.8. I've talked to people who have some experience with them and they seem to have a good reputation. Also overall its around $1000 cheaper than a 9 inch so if I have to do some upgrades to it I have that wiggle room...
Some 8.8 Explorers had 3.73 and some had 3.55 I've even saw later 4x4 Rangers with a 4.10. they pretty much all had 31 spline axles and a locking differential. As far as c-clip eliminators,you won't need them with disc brakes.
If you go 8.8, make sure you get the correct configuration for you car. By this I mean ,check if the rear has a centered pinion or if it's off-set to one side. This will cause major drive-line problems. Good luck.
I have been told and read that due to the way an 8.8" is made it has less rolling resistance than a 9" so you are not using as much horsepower, not that it is a big factor in a decision but something else in its favor.
