Before you try this again, get the K.R. Wilson hub puller from:
Winfield Tool Works
437 W. Broadway
Port Jefferson, NY 11777
(631) 928-3316
Here's a picture of the K.R. Wilson hub puller in action. It turns pulling Lincoln rear hubs into kid stuff (an air wrench helps a lot)! I got mine from Winfield Tools and I highly recommend them AND the puller!
Rear axle assemblies are the same and interchangeable for Continentals and Zephyrs 1941-48. Standard gear ratios are 4.44:1, with or without OD.
Driveshafts are different lengths depending on whether the car has the Borg-Warner transmission overdrive or not. The overdrive unit adds about 16 inches to the transmission length.
A good source for mechanical parts is Merv Adkins, 9655 Hidden Farm Road, Rancho Cucamonga, CA 81737 Phone (909) 980-1332. Merv is listed in the Lincoln Zephyr Owners Club roster and usually has axle shafts and brake drums in stock. May I suggest that you join the LZOC (if you haven't already done so). There's an on-line application form at
www.lzoc.org.Removing the axle shafts requires dis-assembly of the whole rear end, not a trivial task, and is best done with the rear end out of the car.
Good luck!