If you think the rust is only on the outside surfaces, think again. I guarantee you, you will find rot holes in the glass channel. The amount of visible rust on my windshield frame was about the same as Huntsman180, but when I pulled the glass and gasket out, there was a lot of rust and some holes in the channel. You probably don't want to hear this, but to do the job right, the glass and gasket needs to come out.
Here are the steps I took to eradicate the rust on my windshield frame.
1. Pull glass and gasket
2. Scrap every bit of the adhesive out of the channel
3. Send the frame out for a thorough sandblasting
4. Completely coat it with Ospho
5. Spray the insides of the frame with Eastwood's Internal Frame Coating
6. Spray the outside with two coats of two part epoxy primer
7. Fill holes with All Metal filler
8. High build prime and paint
Almost there: '89 YJ with: 390 CID(6.4L) Dodge V8/727 auto/NP231, SOA+2", Hi steer D44 & 14 Bolt w/4.56's, Detroits, 37" Nitto Trail Grapplers