I had a '99 and offer these suggestions:
When putting the cover back on, seal only the upper part. That way, if the drain holes plug, the water can still drain from the bottom.
Also, take the cover to a plastic shop and using it as a form/mold, have them make a new cover blank of Lexan. Drill the holes when you get home.
Bob (Squidly Down Under) & Peg - 2013 Ford Focus pushing a 2011 Phoenix Cruiser 2552S
"In God we trust" to preserve our country and bring our Troops safely home.
Carry on, regardless..................