Bogged down While In Gear And Sputtered During Acceleration

Here's my thoughts. You said it ran good right after you put the new Holley on it, correct?

Then a few days later it started running rough again, correct?

If it ran right for even for a brief time it's not a skipped timing chain. They won't jump back and forth.

Does it have a good fuel filter on it? If not your new Holley is full of crap just like the Eddy was. I love Holley's but have found them to be really touchy about small particles of dirt plugging passages. For that reason I always use a real good fuel filter that filters down to at least 40 microns.