Here is the nine dollar question:
Is the Exhaust manifold a stock OEM unit??
An OEM exhaust manifold can be identified as being an Iron casting instead of an aftermarket header made of a set of pipe runners welded to a head flange on one end and a combiner flange on the other end.
My bet is that you have an aftermarket manifold!
You have now had your first experience in dealing with aftermarket parts problems at the autoparts store.
Although an aftermarket exhaust manifold has it's advantage (more power, doesn't crack open), the auto parts store "don't not know nothin'" about your aftermarket manifold.
This sort of thing happens all the time. I forgot this simple concept recently when I went into an autoparts store looking for tie-rod ends for my Rocky-Road OTT system. Turns out I needed SAE instead of Metric parts -- which would have been a tough search for the O'Reilly database:
"...Rocky Road OTT? Nothing on the computer like that..."
The solution was to call Rocky Road. The tech guy gave me the exact Moog part numbers and I had my steering system installed the next day!
Your solution is to find the manufacturer of your manifold (not all that tough -- either Thorley or Calmini), call them and order a flange. Even better, do a bit of measuring on the manifold's output flange (inside diameter of exhaust outlet, the distance center-to-center between the mounting holes and the number of mounting holes - three is a good guess on my part ;

) and go to the auto part store to find a match. I bet you find a match very quickly!
Oh, and if your friend's exhaust system is stock (as I suspect it is) it probably would not be a good idea to adapt it anyway as going from BIG to small pipe does not help your engine's performance. Your choices are to either find a good stock manifold (possibly hard to do) or spend some money and have a large-diameter exhaust system made for your Samurai (200-300 bucks but well worth the performance gain!).
edit: I noticed that the muffler shop wanted $300 "to replace the muffler". You should be able to simply cut the muffler out and replace it cheaply -- UNLESS -- the rest of the system is so beat up that it all needs to be replaced!
I'd take the truck to another muffler shop (second butte on the left, west out of town

) for another opinion.
Hope this helps!