Hello, after re-reading the posts, I believe we have drifted away from/complicated the original problem of "not charging" by introducing too many variables, new rectifier, different connections, no regulator, etc. I think since nothing has changed you can try this
If you are sure the old rectifier is faulty,
Reconnect the new rectifier into the harness as it should be, not just the brown and black,
reconnect the regulator
check all connections including grounds against a wiring diagram to make sure they are where the should be. Make sure the ground behind the battery box is clean and tight.
charge up the battery and check, 11 something volts is totally discharged, fully charged as noted above will be 13 something.
The ammeter should can be checked for some function in the starting process, does it "flip" when you check for TDC when using the compression release?
Start the engine and check from the alternator back, Is it putting out voltage? How much, is the voltage getting to the rectifier? How much, How much out of the Rectifier? is it getting to the regulator? how much out of the regulator? Are the connections good to the battery? A systematic, methodical search should show where the problem is. Checking a system that is as designed is easier than one that is not. As an after thought, does you bike have the key position that does not allow the system to charge? Maybe that should be checked too. Good luck, have fun, mtrude