Wouldn't it be possible to make the base of the pickup level again using some kind of epoxy resin or maybe araldite?
 
Jazzyvee

Peter, That would be the long term best case scenario.
Jazzy, The problem is the warp age sets the pickups to high in the Bass even with the lower screws removed. Not so much a leveling issue.
A good idea though for repair work.  
~Pete

Years of overtightened adjusting screws is the genesis of this problem. Everyone needs to heed this warning. They don't need to be tightened with an impact driver!  
 
Does anyone have any experience with heating these epoxy castings? I bet a little heat would soften them up enough to straighten them in a jig with a block on each end so that the pressure is even across each ear, leaving them in for a couple of days to do some good. Maybe 150 degrees in the oven for 10 minutes to start, and then increase the temp as courage prevails over caution.

There's nothing in mounting flange area except polyurethane, so you can chop it off and it won't hurt the electrics. There isn't any reason you can't sand down the mounting and get them in the cavities lower. More drastic would be making the routings for the pickups deeper (but do mind you don't punch through the back!).  
 
Sorry John, but the material isn't thermoplastic.  
 
You can buy sets of pickups, and even if you don't replace the humcanceller at the same time (you really should) you should at least buy the correct matched one and keep it safe for when you do have a chance to crack the old one out. Email me if you want any other purchasing details.

Thank you Mica,  
  An E-Mail will be sent.
Peace
~Pete

David,
  You mentioned that the pickups shown are an ?extra set of pickups?, I?m curious did you replace them with a new/used set?    
~Pete

No, I have a project series bass that I have been fooling around with for a couple years and I have been collecting parts for it since i bought it. I have two sets of pickups and will see which ones work best with the existing hum-canceling pup in the bass and then sell the other set. However, I don't know when I will get around to doing it!
 
http://club.alembicguitars.net/Images/411/60995.html?1353883829

As a Follow-up,
  I took the plunge in shaving down the warp age in the pickups so now they rest flat. It was a bit un nerving at first but heck what did I have to lose Bottom line is that by doing so corrected most of if not all of the sound issues I was having and gave me more string clearance. Hind sight always being 20 /20, I should have done this a year ago.  
 
Note: Series Pickups have a funky smell when being grinded and abused.  ??  
~Pete

As the kids used to say, Right on, Pete.