Rob,
I think the wheel covers will definitely impact the value since the Mark II covers are quite unique. However, the impact would be relatively minor since (with some effort) Mark II wheel covers can still be found at a cost of around $3000 for a nice set of 4. Mark II wheel covers can be securely mounted with a relatively modest effort.
The electric wipers are not really necessary if the vacuum system is operating correctly. The fuel pump is also a vacuum pump that will maintain the windshield wiper vacuum even when the engine vacuum drops. If the entire vacuum system is still in place and only the wiper motor has been changed then the impact should be relatively minor since original motors are still available.
The brake system changes are definitely better from a safety standpoint but they do change the look of the engine compartment. Not sure of the impact if you get a buyer that wants to drive the car. The work and parts required to bring the car back to original brakes would probably be in the $3-5K range so not too large for a purist. I changed my front disc brakes back to original without much effort but the prior owner gave me the original parts.
Larry
Larry Durocher
1956 Mark II C5601429
1962 RR Silver Cloud II drophead
2006 Ford F150
2010 RR Phantom drophead
2013 Bentley GTC
2015 Lincoln MKT