Axle Splines a Little Rough??

I removed my axle shafts to swap to new 4.5 axles from the 4.0 bolt pattern. When i pulled out the axles from my current 3.23 gear,8.75 diff,489 case, the ends of the axles are a little rough. By a little rough, I mean the spline on the axle ends look like there was something in the splines or they didnt match up the best and wore the ridges of the splines a bit. Tough to explain, i know. When i feel into the cone style limited slip with my hand, the first spline feels rough but the inner spline feels like it should. I have new $500 buck axles coming and I am a little aprehensive about about putting brand new axles into the centre section splines.
Has anybody run into this before. Do i have an issue with the two splines in the centre section being off just a bit, causing the axles splines to bind a bit.
Appreciate any feedback anyone might have. Thanks.