Since this is your first swap, a word of advice from someone who has done many of them.
Don't worry about the rearend or suspension or interior, or paint, or lighting until you have the engine in, running smoothly, and all the little bugs worked out. Concentrate on one area at a time. If you open multiple cans of worms at the same time it can get to be too much. I had a 94 with a 350 in it and drove it 16 years w/o ever touching the rearend.
If you break yours then go ahead and put the 8.8 in. What is it out of and what is the gear ratio?
There a many variations of the 8.8. The best ones for S10 swaps are the Explorer ones with LSD and 3.73's.
MBP is right about the NV3500 if you're building a driver. You'll need the more expensive options if your building a weekend warrior or race truck. Or have a few grand you want to spend on the best trans available.
If you go with the NV3500, don't get one from a fullsize. In a light S10 the lower first gear used in big trucks will be totally useless. Especially if your rearend still has 3.73 or 4.10 gearing. The S10 version of the NV3500 has a slightly higher 1st gear and is much better suited to the weight of the truck.