I often glue up 30-50 fillet knives at a time. Some have five or six rivet pins.
I tape the scales together and shape and polish the front portion that will be at the ricasso. This area can't be sanded without damaging the blade after assembly, so it needs to be taken to the final grit and buffed before glue-up. Since many of the scales are of the same material, I number them - 1A & 1B, 2A & 2B, etc. This assures the mates will be on the same knife.
The knife blades are all finished except the final sharpening. I put 2" wide blue painter's tape over the blade, up to 1/4" of where the scale will sit. Just put a strip down each side and let the excess stick out past the spine and edge. I usually mark the tape with the knife number to match the scales 1,2,3,etc. If anything needs clean-up, wipe down with acetone, them again with denatured alcohol.
I get everything ready, spread out lots of newspaper across the floor, set a stack of paper towels on the work table, and lay out all the knives and scales side-by-side on the papers on the floor. I arrange them in the order of darkness of the scale material.
I set out a big box of HF clamps in various pressures, all bought when on sale for almost nothing.
When all is ready, I slip on Nitrile gloves, mix 24 hour slow cure epoxy, and start with the lightest scales first. I use HF cheap small clamps to provide just enough pressure to hold things snug, without squeezing out all the glue. I start with the lightest color scales, and use the clear resin. As I go up the darkness scale, I add powdered dye to make it first tan, then brown, and finally black. If I have a few red, blue, or green scales, I pour a bit of the clear epoxy in a small cup and dye it separately. This way all the glue lines roughly match the wood color.
Here is the trick:
As I glue the scales..... I only glue up one side at a time. I leave the other scale sitting right where it is on the newspaper. I put resin on a single scale, set it in place on the tang, align the ricasso as I want it to sit, and clamp with two light pressure HF clamps. I wipe off the squeeze out at the ricasso with a paper towel, but don't worry about the rest of the handle. When it looks right, I set the knife down on the newspaper next to its other scale, keeping them in order. Proceed down the line in darkening order.
I change the gloves when needed, and use paper towels like they were disposable
I have about three hours before the epoxy gels, and four to six before it sets, so there is no rush. When all are glued up, I go back and wipe off every ricasso with acetone to get all the epoxy off the blade part and the front of the scale. Don't worry about the stuff that runs out of the tang holes and gets on the other side of the tang.
When all is done, I wash up and take a break for an hour or so. I come back and re-wipe the ricasso with acetone to get any new squeeze-out and make sure the front of the scale is clean of resin. I make any last minute adjustments to a scale that may have slipped under the clamp pressure, and when happy....I leave everything until tomorrow. Don't worry if it gets glued to the newspaper.
The next day, I take off all the clamps and drop them back in the clamp box. I take the knives out to the shop and give the exposed side of the tang a quick pass with a 120 grit belt on the flat platen. Just be careful to stop shy of the ricasso. If necessary, a little elbow grease and acetone will get any cured resin off a place you can't grind. This removes all the resin that squeezed out and dripped across the exposed tang. When all are clean metal, I go to the drill press. I drill all the pin/rivet holes at about 75% the size the pin stock will be. Because I always make my tang holes 150% of the rivet size I will use, just eyeball the center of the tang hole and you will be fine. When all are done being drilled, I go to the band saw and cut away the bulk of the excess wood. Sometimes I give the scales a quick profile grind on a 36 grit belt to get the scales within 1/8" of the tang. This greatly helps in the final shaping of the tang, as it will let you know where the tang is when the other scale is glued on.
Once all is done, I go back inside.
Set each knife along side its matching scale, set up the work table as the day before with paper towels, acetone, dye, and all supplies you will need. Mix resin, and repeat the glue up of the second scales. After clamping and wiping off the ricasso, carefully check the alignment of the two by sighting across the ricasso from both the spine and the edge. A few tweaks and it should be fine. Set them down in order, and dye the resin as before to match the wood color.
When all are done, clean up the squeeze out at the ricasso, double check the alignment, take a break, come back and re-check everything...and when happy, let it sit overnight.
Next day, I drill out the scales for the pins/rivets, using the holes from first scale to go through scale two. I do it first with the 75% size bit, then with the correct size bit, and follow with a reamer if needed. Then I trim the second scales to roughly match the ones I cut down the day before. Once all pins/rivets fit in the scales smoothly and the scales are trimmed, I go inside and glue up all the pins/rivets. Dying the resin isn't as important here, but I usually still do it. When the resin has cured for 24-48 hours, I clip off the excess and shape the handles on the grinder as desired.
One big advantage of putting in the pins after the glue up of the scales is that you can be assured they all will align. I think all of us have had two or three pins go in fine, only to have the last one refuse to go through the tang or other scale.
Pinning after the scales are on is also very advantageous when using mosaic rivets, as you have time to inspect them and assure they are all "clocked" in the same orientation. In the haste to fit rivets and scales to the tang all at the same time, many folks forget to align the rivets ( or the get turned by accident) and the final knife has one star pointing straight up, with another pointing down.
I find the above procedures, or modifications of them, give perfectly fitted and matched handles in quantity without the mess and difficulty of doing one complete knife at a time.
There are times when I am doing batches of knives where the handle are pre-drilled to fit the tang, as in Corby bolts or two pin handles. In these cases, I use the same procedures, but assemble both sides of the handle in one step. The dying, wiping off, resting, rechecking, etc. are all the same, otherwise.