Yes, the gears will work. Gear sets for the 8.8 are not dependant on the spline count at all. However, you will most likely need to shave a little off of the gears in order to get the cross pin installed (I had to with a set of 4.56's). This won't hurt it at all.
As for the cost of the setup: it will depend on who's doing it, what all is being done (ie, just gears...or complete axle bearings/seals etc), and how fast you want it done. I can setup the gears in an 8.8 fairly easily, but when it came to my D44, I dropped it off with a local shop, still cost way more than I wanted to spend, but it's guaranteed setup. Some places will charge you what the book value is, while some will give you a break as the axle can be put on the bench.