Not Charging after Madd bypass.

Step one in any electrical diagnostics is testing the battery. If that was me, I'd grab a known good one, just for testing.
Didn't change anything?
Step 2: Verify every connection. Describe to us your ammeter bypass. Did you just bolt the two wires together under the dash and tape 'em up? Did you bypass them in the engine bay? Did you hook one to ground and the other to the light in the ashtray? What exactly do you do?
This also includes.....what voltage regulator you got? What alternator are you running? Is the case of the regulator grounded? Is the alternator case grounded? Is the battery grounded? The regulator is plugged in, right?

Step 3, disconnect the direct line to the battery and see what it does for charging voltage. I run mine from the output stud on the alternator to the stud on the starter relay. Why? Because that's what Rick E. said to do years ago. Electrically, it shouldn't matter, but the E-dogg sayeth it for a reason. You DO have a fusible link in this direct line, RIGHT??? Not a fuse, not a breaker, not 'I'll do it later', but an actual fusible link. Test the continuity of said link.

Do all that and get back to us.