First invest in Oracal Teflon Squeegees. Worth every cent. Everything else is crap. Most bubbles come from trapped particles trapped underneath your vinyl Using aluminum draws static electricity and anything in the area you are working on, including yourself, will be picked up when you try to lay down the vinyl on the substrate.
We use those Swiffer Dusters when we work on aluminum. After you apply transfer tape, wipe both sides of the transfer and the substrate before you separate the tape from the backing. Take time to dust yourself off as well. Be as clean as you can get. You can never over do it. Try using a black light one time in a dark room when doing a application and you'll be amazed at what you pick up due to the static electricity. Nothing wrong with your technique just where you're doing you make up.
I struggled with the same problem for years until I took a tour at Oracle and spoke to one of their engineers. He showed me the black light trick. On aluminum, wet is best. Anything you can do to stop static electricity will serve you well.
Even if you do have some small bubbles, sitting your work outside will remove most of them. Scratches can be taken out by using a heat gun on the vinyl.
Good Luck.