You need to get a voltmeter to test the charging system......and your new battery.
First, charge the battery fully. Should be 12.6 V or a bit more.
Then start the bike and test the voltage at the battery.
At fast idle, if it does not read at least 13.4 volts, then the rectifier wasn't the problem to start with......or your replacement is bad. Burned out stators are fairly common.
Have you checked the connection at the OTHER end of both main battery cables ?
You might need a shop visit to get it sorted out.