I'm really liking those knives, Doug. That folder is especially nice. I'm no brainiac and far from experienced with nice folders, but for the screws, here's what I'd try...
I used 2-56 flat head screws for the back spacers on some (failed) liner locks that I was going to put the scales over to hide. The Ti I was using was .050 and I had the corresponding 82 degree countersink. Unfortunately, I needed the 1/4" one, not the 1/8" that I'd ordered. For your back screws (not the pivot), I'm wondering if you could countersink just a fuzz into the back spacer? If you had a few of the screws in so everything was held in place correctly, then carefully countersink, I believe you'd still be able to have part of the flat head holding your metal scale securely.
As for the pivot...I think it would be a little tougher. But, there are so many pivots out there that I think you could find some fairly low profile ones that either have or you could grind the edges down so it wasn't so proud of the scale. If you counterbored just a little bit into the scale, it'd still hold well (I think...) while bringing the thickness at the pivot down a bit.
I hope that makes some kind of sense.
On another note, I might finally get to meet you-I'm heading to the Seattle show with Bing. I'm really looking forward to getting to see so many great knives and makers. Matter of fact, I'll bet he might have some good ideas for your folder screws.
Jeremy