The air bubbles are in the rotary valve chamber lines. It is no big deal, Its just for the oil sump for the Rotary Shaft in the crank cases. The oil injector lines shouldn't have any air bubbles. Be sure the ground wires are clean and getting a good connection. Here is some info on the charging system;
When the engine is running, set your voltmeter for 20 VDC and put the leads on the correct terminal posts. With the engine running, you should be reading anywhere from 14.5 to 14.8 VDC. (typically this test is done at 5,000 rpms) This tells you your charging circuit is good. If the voltage is higher, the regulator is bad. If you’re not showing a charge and you've replaced the rectifier, you may want to do a test on the Magneto/stator/charging coil. If you’re not a premium member and you don't have access to a manual, this test will be hard to do without it. There are 2 fuses that protect the charging system. Check the 15 amp fuse in the MPEM and the 15 amp fuse between the solenoid and the MPEM.
The magneto and stator create un-regulated AC current. The "rectifier" converts that AC to DC current and the regulator maintains the current between 14 to 14.5 volts DC for the engines operation and charging circuit.