Must have been a terrible feeling. Best of luck with your repairs.
I have the Trailex trailer that was custom modified for the PocketShip. On the Trailex (at least the one I have) the three parts of the keel trough are separately mounted to the trailer, so I can easily remove the bottom of the trough and leave the sides in place to guide the boat onto the trailer. I have ordered two rollers with brackets that are exactly the same as the roller at the back of the trough. My plan is to replace the bottom of the trough with two rollers, for a total of three, and as I said the trough sides will still be in place. I have written John Harris about this plan, and while not exactly endorsing it he has said the keel is plenty strong enough to be supported by the three rollers without incident. If it does not work out as planned, I can always replace the trough bottom, but I plan to drill some drain holes in it at strategic points.
I can see several advantages to the rollers vs. the carpeted bottom: Good drainage, obviously. The ability to easily inspect the keel bottom for wear and damage. Easy access to the keel bottom for repairs and repainting. For this purpose the trough sides can be temporarily removed, and the boat can be moved forward and aft a few inches to gain access to all parts of it, while making sure the hoist line is attached to the bow eye to prevent rolling it back too far.