Slant Six Tuning/Running Issues

Not necessarily. To me, it kinda sounds like a timing thing, so I went for the quickest item to check. Next I would check the cap and rotor. Just cuz it's new doesn't always mean it works.

What am I looking for here? The cap fits well and the hold downs are tight. Would pictures of the cap and rotor help with anything?

Have you removed and cleaned the gas tank? Getting the entire fuel system clean, clean, CLEAN would be the first thing I would do. Also inspect and or REPLACE all of the rubber fuel hose sections with new and make sure the fuel filter is new. Even if it is, with a nasty fuel system it can and will clog again. Without all that eliminated, you may just chase your tail.

Tank is new, All lines are new (hard and soft), and a new quality filter. The pump is the only thing in the system prior to the carb being reused. It was flushed before hooking up the the carb.