ARRRGH! It's not the alternator, Help!

[Big Red]

I have a new battery, for a long time it seems that the car just won't charge the battery, I just had the alternator checked and it passed with flying colors (not bad for the original 200K unit btw).

I need suggestions on what to do next, I did a valve grind and gasket change and timing chain swap about 5k ago and I may have knocked something loose.

The car had a harder time starting recently and now all of a sudden it won't charge the battery at all.

Please help!

[Big Red]

I did a test and found I had a slow drain on some aftermarket wiring that was done so now that has been disconnected.

Here's what I found, using an OHM meter I attached one to each of the battery cables (no battery) ZING! no resistance at all untill I pull the ALT fuse and then it drops to 2ohms untill I pull the ENG CONT fuse, when I do this I finally get an open circuit but I still don't know why the battery is not charging.