Clear primer and cement is a VERY good idea. Especially if you're gonna glue anything inside the tank. A little drop of glue or primer inside the tank and you'll be looking at it for a loooooonnnnnngggg time.
I didn't even glue the loc line and manifold inside my tank. It comes apart sometimes, but I don't care. I was just too scared to go anywhere near the display tank with glue and primer.
If I had it to do over, I'd put bigger pumps. I'd go 12 X turnover, maybe even more.
I went without the pond boxes, and I haven't notice any ill effect. But, I have a drip system, too so I might just not every notice, or ever really put any load on the bio-media.
I'd go with a 3 inch gate valve and T. 2 inch siphon drains into a 3 inch T and Gate Valve would have been PLENTY. I didn't need to put a 4 inch gate.
I'd have bought the skin for the stand. I used to LOVE looking at the sump, and I have fish living in it now, but I'm gonna end up cutting and covering some panels to cover up the sump eventually.
Lights--I still have crappy Finnex LED's on top of my big tank. Just never got around to buying some good lights. I'd like to get some custom made lights, and nice hanging kits.
Bigger. I'd have gotten a bigger tank. Seriously. You get an 8 foot tank, you think you'll never need a bigger tank, and as soon as you get it stocked you start thinking it's not big enough. That's because...it's NOT. I keep Vieja and Ampn's--these fish need really big tanks. You can keep 1 or 2 in a 125, maybe 3. But they really need a bigger tank to move around, fight without killing each other, etc. I wish I had a 10 foot tank, or a 12 foot tank, 48 inches wide maybe.
I hear ya...there are a few things a would do differently that's specific to my peninsula as well. I don't have more room for something much bigger, but little design changes and tweaks to how I used the internal overflow space...