For that crank on a 68mm BB shell, you should be using 2x 1mm spacers, I think. The 2.5mm spacers are if you want to use a MTB crank on a 68mm shell BB.
If the crank is (still) hitting the frame, you might be able to fix it by putting both (1mm) spacers on the drive side. By moving the non drive side in 1mm, you would get 1mm more. If that isn't enough, then you're screwed (or into soem serious engineering), but if the crank was ok before, it should be ok.
You probably haven't deformed the splines on the crank as they are steel of the highest quality.
There should be no side load on the bearings in GXP bb - the drive side bearing should not be pressing against the crank at all. By using 2.5mm spacers, you've got the axle attempting to squeese the bearings together, and that is wrong. The axle should be clamping to the NDS bearing AND THAT IS ALL!
Installing the GXP adapter bushings can be a bit of a hassle. Personally, I install the bushings before putting the NDS bottom bracket in the bike. If you use the crank to compress everything together, is fairly easy.
The hope bb attempts to keep dirt away from the bearing with the plastic thingies which have their own channel to run round in (which is quite a nice design, IMO). When they are new, the plastic rubs on the channel a bit. After a while, the plastic wears and everything spins more freely