You might be able to use the flange from a Mustang 8.8. I'm pretty sure that they are smaller than the truck flanges. There are standard yokes availbale for the 8.8 too. As for the pinion depth, you won't change it, but you have to be carefull not to change the pinion bearing preload. The best way that I have found to do this is to torque the pinion nut to 125 to 150 foot pounds. That is tight enough to keep anything from moving but not tight enough to crush the spacer any more, which would increase the pinion bearing prelaod. I'm sure that someone is going to tell you to mark the nut and count the number of turns it takes to remove the nut. That will not work when changing the flange because the replacement flange will not be exactly the same thickness.
When replacing the flange or yoke be sure that you smear a little RTV sealant into the splines of the flange or yoke before you put it back on. If you don't then you will have oil seaping out around the splines and around the nut. Do not put sealant on the pinion shaft splines. If you do you will push the sealant into the outer pinion bearing when you install the flange or yoke. Also use red Locktite on the threads when you put the nut back on. Using a new nut is a good idea too.
The S10 drive shaft has Mec 3R u joints. To remove them you heat the yoke until the plastic squirts out the holes. The press them out.