My take on what they told you applies to the newer vehicle. The emission control rules in some states are such that muffler shops will not make modifications that will impact those rules and thus will only do mods from the cat converter back.
Their reply does not pertain to your 1946 truck. They will probably be very happy to set you up with a new system. It should consist of a cross over tube or X pipe between the two pipes and then two mufflers followed by rear exit tubes over the axle. I would not recommend side exits as the noise level is louder in the cab.
I have found a shop here that will do the plumbing for $200 while I supply the mufflers. With mufflers included the cost should be between $300 and $400.
The diameter should be either 2 1/4 or 2 1/2. I am going to run 2 1/4 on my 350 set up. Larger than 2 1/2 is not necessary.
If you are looking to increase the power in your 2001 then a computer chip or reprogrammer should be your first step.
Are you in Korea now? If so - stay warm.