Lots of questions here....
I looked at them and searched and don't think it's available in 5.5" width and don't see how to make the 3x4" work. You are correct. 3x4 gutter downspouts won't work for a 2x6/
I may be able to get a couple pieces of used Trex wood decking my thoughts on that are;
1. can I counter sink screws to attach it without removing the carpet from the 2x6"? ...I don't see why not. The only issue that I see would be that the Trex is probably 3/4 inch thick, so you will be raising your bunks by 3/4 of an inch. That means you will have to back your vehicle in more to launch from the same place as before. Also, you would want to taper the forward edge of the Trex so your boat wouldn't have to deal with a sharp "drop off" when launching or recovering.
2. is it as slick as vinyl or PVC since it is used as decking is it slip resistant? It's been a while since I looked at Trex (they dramatically changed its formula after a lot of complaints) so I cannot properly answer this question with any personal knowledge. In my opinion, though, I think it will be plenty slippery as is. The "wood grain" that was on the original Trex wouldn't stop my boat from sliding.
The PVC garage door trim looks like a good idea if I spend $40.00 Yes, but it has the same issue as the Trex. It is 3/4 of an inch thick, I think.
What about the lattice Rich, did you rip the 4'x8' sheet into 3.5" or in my case 5.5" strips and how did you attach to bunk? The lattice that I used on my very first venture into adding "slickness" came in 4x8 sheets from either Lowes or Home Depot. I ripped the diagonal strips to get as long lengths as I could. Hence, the longest strips were about 1 1/2 inches wide and about 5 feet long. I used two or three strips (wide) on each bunk. To mount them, I countersunk Stainless Steel screws. After thinking (and worrying) about that mounting system, I went back, pulled the SS screws out and put Stainless steel bolts and nuts in their place. I worried about the screws working their way back up and ruining the bottom of my (then) fiberglass Carolina Skiff.
As far as covering 2x6 bunks, I have thought about buying some vinyl siding, which comes in 10 or 12-inch widths. I'd rip the siding into approximately 7 or 8-inch strips. Then if a smart guy could figure out how to heat a long wire; lay it on the vinyl for a while, he could bend the PVC siding so that it would have a 90-degree bent edge on each side. It would then look, and act, just like the vinyl guttering. I believe it would be a bit thicker than the PVC guttering, too, but not as thick as the 3/4 inch found on Trex or the PVC boards.
Since I don't have 2x6 supporting bunks right now, I haven't pursued the vinyl siding bit.
Hope this helps.