Not yet mentioned is the new cassette's high cog size change. As the cog looses teeth the gap from the guide pulley and high gear cog increases. More open chain is more chain links to flex before the chain climbs off the next small cog and onto the small one. This aspect changes with which front ring is in use, the rear cage's wind out changes the guide pulley's proximity to the cassette.

When the 10 speed wheel was installed were there any other chances? Like the cassette, chaindérailleurre, cable/casing, shifter? As kimmo said you need to establish the baselines properly. We don't know if that has been done well with whatever else might have been changed.

Could the alignment be part of the problem? Sure but as cny-bikeman mentioned chain lineline (rear triangle alignment) is not likely to be the big reason. Hanger alignment more so. But i suspect there's more going on that has not yet been said or corrected. If the frame was spread to fit a 10 speed wheel then likely the bike had a different spec before and the shifter, cable, casing, chain were all changed too. If so why not include this info in the OP?

The first thing i do in these cases detachetatch the cable completely and adjust the limits to shift fully across the cassette with my hand pushindérailleurillure. While this adjustment is not the final onexerciseersize does give you information aboudérailleurslure's movement and shifting action independent of the shifter/cable/casing.

The bike can only be seen and touched by the OP. It's up to him (her?) to figure this out or go to a LBS and ask them for help where another more experienced hand/eye can deal with this. Andy.