I always seemed to scratch the blade no matter how careful I was or what kind of cloth or Q-tip I used, so I came up with something a little different. I hope I can describe this properly without pics..
With the scales off, put a 2" wide strip of blue painters masking tape on each side of the blade, covering the entire blade portion and running partway under where the scales will be.
Then put on the scales (over the tape) and tighten them down (if using corbys) or clamp them (if using pins.)
Using a box cutter with a sharp blade, score the tape right at the front edge of the scales.
Then remove the scales and peel off the portion of the tape that was under the scales.
Epoxy and re-apply the scales. Use a paper towel and rubbing alchohol or acetone to clean excess epoxy off the front of the scales.
Every 15 minutes or so, check to see if more epoxy has oozed out and clean the front of the scales again if necessary.
After about 45 minutes or so, when the epoxy is not fully set but has stopped oozing out, peel the tape off.
Perfect every time!
Note: Don't bother applying tape to the front of the scales as well to keep epoxy off them - it doesn't work well.