If you read the Minton Mods and compare them to a 35mm fork damper rod once you have it out and in hand, you'll notice some discrepancies or errors in the article. Minton calls for slightly enlarging the small upper hole and drilling through the rod to create a second hole, all using a #54 drill bit. As you (and I) discovered the stock little hole is already bigger than a #54 bit size. All I can figure is the bit size numbers got transposed or switched from 4-5 to 5-4 when the article went to print. Well, that's my theory anyway, and I'm sticking to it, lol.
The other error concerns the larger bottom holes. Minton says you'll find two 1/4" holes and instructs you to drill two more so you end up with a total of four. Well, there are already four there, at least there have been on every 35mm damper rod I even saw, but they are a little smaller (near 3/16"). I decided to use a #1 bit because it is slightly smaller than 1/4" and I happen to have a good supply of them (we use them at work). I figured I could always easily go bigger if need be but it's much harder to make the holes smaller again. Well, it seems the combination worked well, so I feel no need to change it. I guess I just got lucky, hitting on the ideal, or near ideal hole sizes.
Minton says that these later 35mm 650 forks aren't too bad for the most part but they don't respond well to little bumps or just one bump. Once you get them pumping they're fine, they're just a bit reluctant to get started. Little stuff jolts you through the bars instead of the forks soaking it up. The Minton Mods fix this. The forks become much more supple and now work over the little bumps better. This makes normal, every day driving much smoother. I can't say I notice much, if any, change or improvement during high speed or aggressive riding, but it's no worse either.
I know 3M has said he doesn't approve of these fork mods anymore and is even considering taking the whole Minton Mod article off his web site. Maybe they're not the best choice for racing but for daily driving, I quite like them. I'm sure spending like $200 on emulators and custom wound straight weight springs gets better results, but this mod is basically free - and it does help.