New parts may not be perfect...when replacing a rear der hanger always check the new hanger's alignment...i've installed many that were not aligned correctly and required some tweaking.
Start from the beginning...check new rear der hanger alignment...make sure the new chain is the correct length...unless you are using a cassette with a different tooth count you should not have to adjust the B limit screw unless it was not adjusted correctly before hand but it doesn't hurt check and adjust again as necessary, at worst it eliminates a possible source of trouble...check and adjust H and L screws on the rear der...check der adjustment/cable tension, adjust as necessary...
As an afterthought was there a spacer between the old cassette and hub that perhaps was not used when installing the new cassette??? just a thought...I've done it in the shop and spent several minutes wondering why it wasn't shifting correctly...looked at the old cassette and there was a spacer stuck to it...popped off new cassette...put spacer where it belonged and voila shifted as it should...just a 'duh' moment but it happens...I always make sure to check for a spacer so I don't waste time doing a 'duh' again.
Good luck and keep us informed...

and yes apparently i love using '...' far too much...