I can't speak for WK, but I've installed several sets of their sliders and we've been working on our own design for the last 6 weeks so there's some knowledge crossover -
1. If the mounting plates sit flush and you didn't have any gaps under the brackets, shims shouldn't be necessary. The frame in regards to that area is the same for all 2014-18/19-24 trucks so I don't know why that is an optional element, but there's likely a reason they included it. There are two nut-serts in the frame that pertain to the diesel DEF crossmember, it's possible that their mount lands over that on the gas trucks and the shim has cutouts for the nutserts?
2. In my experience it's good to torque them to spec, but some are a total bear to really crank down on. The lower bolts are the most important - they are what keep the slider from sliding up on the frame under impact. In the past I've gone to 90ftlb, it really deforms the brackets at that spec but holds them really well. I would try 60'ish on the brackets you can get the torque wrench on if that's what they've spec'd and see how it works.
3. The front brackets are notorious for this - it's not WK's fault, there is so little room between frame/cab in that area, and there's so few areas to put a mount in the forward part of the truck. Without going to smaller diameter hardware you can't avoid it in that location. Generally installing the upper bolts without washers in the area under the sheet metal depression that hangs lowest will help. The real fix is to just find a really nice bump in the road and smack it

The cab will move down and the hardware will dent that little spot in the cab underbelly, usually ending the squeak/tapping noise for good. It's harmless with no ill-effects and is the reason most people simply stop hearing the noise - they hit a bump well enough to put a little dent there without knowing it.
WK makes a phenomenal set of rock sliders, you should be very happy with them!!