You're on the right track again Josh---glad to help or have helped!
Yes on the acorn nut tightening tool and process. I also have fairly strong hands and can/have been a bit too eager tightening those nuts so have learned my lessons from the resulting breakage. If they're drawn down evenly, a few 1/4 turns each time on each nut will get this done easily enough, no breakage.
Assuming you have "warm" days of at least 70* F the Window Weld is compliant enough to squeeze out, not really requiring a huge clamping force to be effective. (As a butyl sealant it adheres to whatever it touches, being a solid sealant gives it its sealing properties.)
Once the windows and spacers are removed you'll see how the OEM sealer was applied. Channels in the spacer are designed for this sealer and allow the round cross section to spread out as its compressed via the mounting bolts & acorn nuts. The door shell flange and naturally the glass are both very smooth surfaces, the spacer channels controlling the sealant action as its all tightened and drawn down to mate up.
The only real way to view the squeezing effect would be from the inside as you're tightening the acorn nuts, from that same side. I'd not use a 3/8" ribbon sealer---too large. I prefer instead 3M's 08610, 1/4" OD because it's more than sufficient and is less risk of breaking the glass. Honestly a 3/16" sealer would do this job perfectly.
Your experience with feeling and paying attention to torque rising as a fastener is tightened will serve you well here. I'm not trying to scare you off this job but slow and steady wins this race. When I've explained this in the past here I've recommended anyone the least bit skittish or unsure about this as a DIY project use a high quality exterior grade silicone sealant/adhesive due it's almost infinite ability to conform to surfaces with little or no real clamping force required. Here's an example: http://www.caulkyourhome.com/sealing...and-energy.php
IF there is any breakage I can possibly arrange a new part purchase with my discount. Hopefully that won't be necessary but a phone call would be the ticket if and when. Not trying to jinx you, just trying to cover all the bases.
You'll do fine with this I'm sure!