Just to check, did you replace the diff cup inside that holds the spider gears as well? The pin that holds the spider gears wears grooves in the plastic cup that allows the spider gears to get out of alignment and cause binding.
Also, what center axles are you running? I had a clicking noise that was coming from my cvd's. Where the dog bone end connects to the tranny, the dog bone ears wore grooves in the tranny outdrive. When the axle turned, the ears would go into the groove and pop out of the groove due to the angle the axle travels in. I replaced the out drive cups and the problem went away.
Also, if your going to rebuild the diffs, I would suggest replacing the spider gear plastic cup and ring gear with a Maximizer Aluminum Diff Cup and modified stock gear. It's made out of 7075 al and doesn't succomb to the wear problems the stock plastic one has. It's not cheap, but it's worth it in my book. It makes the diff gears last much longer.
Case in point, within one gallon on my 21 maxx, I had to replace the diff cup and ring gear 3 times. Just before I started gallon two, I replaced the stock ones with the Maximizer cups and I have 1 and 1/2 gallons on it now. I took it apart before I started the 1/2 gallon and there is absolutely no wear on the ring gear, spider gears or the diff cup.
You can find the diff cup @
http://www.lightninghobby.com/store/viewitem.asp?idproduct=3747