Making Solar Panel mounts, what thickness angle iron?

I would for sure go with 1/8" aluminum and 2" x 2" stock. Remember to keep some airspace between the panel and the roof so anything shorter might see your panel physically touching the roof membrane. If the "L" stock is bolted onto the side of the panel its likely going to leave you with 1/4" or a bit more gap and flush with the top of the panel on the side depending on brand. That should work out about right.