So what's your favorite way of replacing fuel tanks on a GB49?

Up through the engine hatch.

You will need to pull at least one engine.
You may get away with temporarily moving the other engine onto the opposite
mounts,
(and then back again, obviously) when the new tanks are installed. Depends on
space.

How do you plan to use the boat? Many trawlers have a lot more fuel capacity
than they need. A boater running 75 hours a year has too much fuel on board
with 450-500 gallons, yet you run into these situations all the time. You could
possibly make your life easier if you could use slightly smaller tanks. Going
to smaller tanks could impact the eventual resale value, however, and its
defintiely not something you'd want to do if cruising the length of the ICW is
part of your plan for the boat.

The bladder option may be less desirable on large tanks. Bladders don't have
the internal baffling that helps control slosh in partially filled tanks. Way
more than OK on a 10 gallon sailboat aux application, but
unless there's some way to baffle bladders that I don't know anything about I'd
be careful on a 150-250 gallon tank.

You found the tanks at the *right* time.
You have a lot of leverage to get the seller to make the repair. After all, if
the seller lets you "walk" over the fuel tank issue, he'll simply be dealing
with it again in several months when (if) he finds another buyer, who will also
want the boat surveyed.

You are well aware, of course, that unless
the availability of cash is a key issue that makes it more convenient to roll
repairs into a boat loan, you're better off to get an estimate from a
legitimate yard, (add 20% for aggravation and the inevitable "discoveries" as
the job progresses), and get a financial concession from the seller.
The seller will be more likely to grant a price concession than to screw around
doing repairs on a boat he's mentally done with. If the seller does attempt to
do the repairs it will likely be a quick and very dirty job- not at all what
you want.