Thanks, all. Scramps- now that's rusty.
I know my tubes aren't bad at all, but here in SW ColoRADo, metal hardly rusts. So by our spoiled standards. And I won't be re-using the stock headlight brackets so I need to figure something out to deal with the rust. I've seen people run the stock fork boots and then wrap the section between the trees with hockey tape or bicycle handlebar tape. But that seems like it would accelerate the rust.
Frank's Forks charges $339.00 + shipping for new tubes. I've heard they are excellent quality but I don't have the coin. Custom tubes 1" shorter than stock would be rad though. So I can drop the front end a tiny bit for quicker handling (and looks, not gonna lie, plus my wife is 5'2") and not have to have the fork tubes poking up above the top tree.
I think I'm going to do what evinrude7 and Flyin900 suggested and get the section between the trees down to bare metal, then put down a coat of black rust eliminator paint (had great luck with that stuff on my VWs) and then a coat of gloss black. The chisel tip is great. I may also wrap the tube in cellophane and see if I can still slide them through the trees, then remove the cellophane.
This guy painted his gloss black and it ended up looking not so bad:
b52bombardier1- the JB Weld idea is also intriguing.