Wow, that is going to be one sucky job to do.
I have seen the fuel tank on my friends E 32' so I know what miserable access you will have without dismantling part of the cabin sole.
You might check Roger Long's blog about his E32 "Strider"; he did quite a bit of a re-fit on his boat but I'm not sure if he re-did the fuel tank.
The design called for the fuel tank to sit in the lowest of the bilges just forward of the engine. This might make sense from a weight perspective but does not make that much sense considering that the fuel tank is made of metal (perhaps Monel?) and is likely to often be wet. I'll assume that your E32 is also the shoal draft version?
I wonder if it would make sense to place your new tank(s) a bit more forward where the bilge is much shallower, under the cabin sole. If you did this you could then add some lead weights to the now (hopefully) empty deep bilge to compensate for the weight of the fuel tank moving about 2' closer to the water line. You could contact Roger Long (he is a retired Naval Architect after all) and ask him what he thinks about this idea (or I could contact him for you, if you like).
This could be a chance to also re-do your cabin sole if it is starting to look "tired". I really like the cabin on my friend's 1982 E 32, but I dislike the plastic Beckson ports. His 30+ year old ports need replacing badly.
The original spec says the stock fuel tank held 20 gallons of fuel. Without doing the math I'd guess that the weight of the fuel would equal about 150 lbs of ballast being moved higher.
ENDEAVOUR 32 sailboat specifications and details on sailboatdata.com