1. Structural integrity of separated “Cap” and “Base”: Original plan was to have a Base box and a pop-up Cap. So I built Base first. But for various reason, ended up with attaching Cap (2-ft high) on top of Base (4-ft high). The problem is that the studs in Base and Cap (2 by 3 lumber; every 2-3 ft along the wall) are not single 6-ft long ones, but separated between Base and Cap. I plan to connect/enforce it with 6-ft long studs inside the wall, maybe 3 on each sides screwing on the existing studs. Would this be OK against strong winds from sides?
I think I'd add a few metal 'L' brackets where they join, just to be on the safe side. But remember that wind can do whatever it wants. Also, Semi trucks will naturally create a wind that will push at those 6' sides. Therefore, I would also get a set of sway bars for your tongue/hitch area.
How will you seal the area where the top and sides come together to keep water from getting in? A thick layer of PL2000 construction glue?
2. Structural integrity of Cap ceiling: I’m building a ceiling: foam(1.5”) + internal plastic panel (1/8”) + outside wrapped by canvas cloth with Titebond-coating (called poorman’s fiber glass). The frontal side is slanted (25 degree). Vehicle height is 5.5-ft, leaving most Cap area (2-ft high) above the vehicle. Would a ceiling (without solid cover layer like plywood) be strong enough during 70-MPH on highway?
If it's not too late, I'd turn that top around so that the curved end is in front instead of in the back. It's more aerodynamic that way and will save wear and tear on your tow vehicle as well as saving MPG. It will give you a wind assist of sorts instead of fighting the wind so much. You can Google "aerodynamics, slant or curve" but if you go into the depth of the concept, gets into complicated reading.
3. Anchoring/locking mechanism: Currently 6x12 wide and 6-ft tall structure (950 lbs) is simply sitting on a 6x12 utility trailer. The trailer has a layer of treated lumber floor. There are about 1.5’’ gap between the camper and the metal guard rail on each side (if necessary, easy to fill this gap by inserting boards). Would you suggest good anchoring/locking mechanism between camper and trailer?
My personal opinion is that I don't see how the guard rails are a problem but I would definitely anchor your cabin and deck to the trailer. That may be difficult since you've already sealed up your walls. Usually, the wall sides/deck are bolted to the chassis before the inside walls are put in. You may have to get creative.
One last note: It may be an optical illusion but, while your trailer fits in the garage, In picture #2, it looks like you might have to let some air out of the tires to get it through the garage door. Have you pulled it in and out of your garage yet?
Thanks for the pictures. They do help!
Once again, please remember that what we advise here is just personal opinion. Most of us are neither engineers nor gods,

You are ultimately in charge of what you decide to do. Even with pictures we can't see nor know everything. Best Wishes!