[67 Burb]

You said "6 Gauge wire strait to the battery. It charges with no issues." Why do you think "Obviously it has to do with the ALT right? It ran fine before hand."

If it charges fine with the new alternator, then what's the problem? What makes you think it has to be the alternator? What is the voltage showing while you are driving. The alternator not charging shouldn't affect the way the engine runs. It will run off the battery just fine.

Verify the charging system is the first to do. Hook up a volt meter to see what is actually happening.