Update: I went back and checked the air pump again, pulled the power plugs and reattached. I had a corroded connector on a front park light and cleaned that up, reconnected. Now everything works *scratching head*.

My fuse diagram doesn't show the parking lights being on the same circuit with the door modules, so I'm thinking that perhaps one of the connectors on the pump was loose or is also corroded. I'll have to check that again, though I'm not in any hurry now as I am enjoying having window functions again!

__________________
'98 E300 Turbo Diesel 274,000 miles