I dont' follow exactly what you intend to do, but mine looked almost exactly like your picture at that stage. I then mounted 1/8 stainless flat bar on the top of the rails, this was flush with the joinery inboard but overhangs outboard by about 3/8 inch. An HDPE slider was sawn on a table saw to mate with the SS "track" and the plexi screwed to it using machine screws ( you can drill and tap the HPDE). It slides under s spray hood forward. The rails are only just high enough to allow clearance for the HDPE slider. Now mine got a little complicated for other reasons: I made the plexi crowned for drainage and to match the deck, the hatch is offset so one rail is lower than the other, the spray hood needed to be really thin so it is carbon fiber, etc. But the concept has worked very well so far. I made the tolerances a bit too close to begin with and when it was cold the hatch was very stiff to slide. We opened up the tolerances and now its great, no rattles or anything. Sadly I do not seem to have a picture that shows it, but this is the drawing we started from.