I never had much luck with glue, and that stuff sets in 5-12 minutes, Yikes! I would make a mess of it
I'd drill straight on through from one c-beam into the next. Through hole in one, tap the other or a not, depending on whether or not you need the space.
Success should never be contingent on luck, but rather ... on preparation. Start with your side plates attached to the lowest layer and then all you have to do is lightly coat the mating faces and drop in the next layer. Push down to squeeze out any unnecessary epoxy, align the ends flush, and clamp the heck out of it. Easily achieved in 5 minutes or less if you stick to one layer at a time. Be sure and verify layer thickness with calipers before epoxy sets. Another option would be merely bonding the face plates to the extrusions. Build and square the assembly dry and remove and epoxy the plates one at a time. Won't give you quite the bond as the other approach but definitely more fail resistant. BTW, one of the keys to epoxy is moderate temperature so do this in as cool of an environment as possible. In a 100° F shed you'll be lucky to get even 5 minutes.
Looks good, That thing is a tank. You need a good mister for aluminum and avoid slotting when possible. My mister is similar to the one in this vid but has a tube within a tube. The center tube is the coolant and the air flows down the outside tube. I run it at 60psi and it clears all the chips and keeps things cool. I haven't had any welding with it yet. I use an O Flute bit
Yeah, I don't have the space or the budget to do what Wade has done, but it's an impressive machine! Very well designed. At some point I'll move to a Y table like his, but one step at a time. The question now is, can I find bearing blocks like the ones he used, for my lead screw. I think those bearing blocks were part of his ball screw package. I'll probably mill my own, gently. Yes, he's clearly learning how to use a CNC machine, it's his first or second run at things. But he certainly has machining experience. Anyway, I though I'd share. There are some pretty cool elements to his rig.