I think you did the right thing. That is a standard channel and plastic strip, fairly readily obtainable except for getting a long continuous section.
Seek out stainless screws of the same size and thread pitch (which may mean quite a bit of searching) and use butyl tape underneath the strip. Run the screws in, and walk off and wait as the butyl slowly works its way out, gently snug the screws (by hand) and do this till you think that all the excess butyl has come out. Install the plastic strip and MASK the top seam of the retainer (with blue painters tape, both above and on the strip and run a bead of Dicor non-leveling sealant. Dont run a long bead, keep it short, a couple or three feet, then use a Popsicle stick to form and remove the excess. Continue on. If you go too far, it will start to skin over and be difficult to smooth out and remove the excess. You should end up with a small filet seal along the top of the strip.
'03 Ram 2500 CTD and 2008 Bigfoot 25B21RB.. Previous, Being repaired and will be sold, is a 2008 Thor/Dutchman Freedom Spirit 180. SOLD - 2007 Winnebago View 23H Motorhome.