Ive made some progress. I have two baffles yet to put in after a second water test. Here is the order of how I put the baffles in.
Friday evening, I put in the lower baffle that separates the drain chamber from the fuge. I let that cure for 24 hours.
Saturday afternoon, I performed a water test of that chamber. I decided to wait on the upper baffle of this set until after the water test, so that if I had a leak, it would be easier to get to with the caulk gun.
Drained all the water out and dried things off really well. Set up the upper baffle for caulk. I used cut pieces of wood to maintain 1" gap between baffles and 9.75" wood on the chamber side. I used CD cases to maintain 1" under the baffle. Finally, a clamp to keep the glass against the wood braces. In hindsight, this was overly elaborate. Caulking this baffle proved to be a big messy disaster. My contraption with the hose failed. The gun could not provide enough pressure to push the caulk all the way down the hose because the hose stretched. Eventually, I had so much pressure in the caulk tube that the caulk busted out the back of the tube all over the piston of the gun. I thought if I used more rigid tubing that might solve my problem, so I took a trip to menards. Using rigid tubing was better. It got the job done, but still had the same problems. I wasted a lot of caulk out the back of the gun.
Final picture for now is of the left upper baffle caulk in as well as the first right baffle. I used a different method on the right baffle that proved to be way easier than cutting wood braces. I just used painters tape on one side of the baffle. Two pieces on each side and 3 on the bottom as well as one piece on each side where the top of the baffle meets the side wall. I caulked the other side, checked for alignment, and let that set for an hour. Then I took the tape off and caulked the other side. Worked like a charm and saved all the extra measuring and cutting. I would recommend this method.
Currently waiting on a full cure before I water test the center chamber. Once that passes, I will get the remaining 2 baffles into place.