Windshield moulding clip retainers (nails) gone

[Patdown45]

My 1966 hardrop had the windshield removed when it went of for body and paint. When I finally got the car back 3 years later, not only was the engine seized (he left the car out in weather with no hood or air cleaner, she drank alot of rainwater. Fixed the motor, but noticed all the nails that the windshield moulding clips attach to the body are all gone. They appeared to be welded to the body. The channel is got fresh paint now and was wondering if there is some way to drill and tap some really small say 4-40 threaded holes and install some small fasteners to hold the clips? Or am I overthinking this is there an easier solution? The windshield installation is scheduled for next Friday and I don't have any of the clips or nails yet, I think this will be quite difficult once the glass is in, any help will be greatly appreciated I will try to add a photo of the channel as it sits now