I think the only thing Bigfoot used on the sides is butyl tape under the flanges and silicone on top. So if there is some Hengs or other on side bits it was done aftermarket. I personally wouldn't use that stuff for anything but I'll admit I am way in the minority.
The two halves of the shell have an overlap, the top overlapping the bottom. The trim piece covers the joint and also hides the screws. There is no feasible way to recaulk or improve this seam. However the screws can leak and eventually rot something. I don't know when the crossover was, but originally they used steel screws and then changed to SS screws. I would check yours to see which, if steel I'd go to the trouble of replacing them all with SS, sealing each one with a little PU sealant. The silicone normally spread around that trim does absolutely nothing except collect dirt and mold.
Resealing windows is a lot of work, I'd do what Jim suggests to start with. Also good the clearance lights, they have very little flange sealing them and if the wiring hole was drilled a little bit off, you have leaks. The later models have a very sticky, stretchy sealant that you hate to disturb if it is still good, so it is a dilemma - disturb what may be good or leave it alone until it actually leaks.