There's only 1 way that you can run the header evac system with mufflers or baffles that i know of and that is to install the tubes behind the mufflers or the baffles, they will not be as effective as collector installed without mufflers or baffles, but will work. If you've ever blown air across a glass of water you know it will suck the water out, the more air you blow the more it suck the water out, same theory with the header evac system.
In the old days we didn't use header evac systems we just ran about a 4" tall tubes and breathers, i've run blower motors that way in the 60's. Now aday i run burn down tubes 1 1/4" dia into a 1 gal catch tank with the blown alcohol motor with zoomies, but i run a 1471 on a small motor.
I've got a set of zoomies with evac system plumbed into all 4 tubes on each side but i don't think i will use them. I bought them from my friend up in Oregon with the Willys convertable.
Zip.