When budgeting for boat projects, I use the "rule of three":
How much will it cost? About three times what you estimate.
How long will take? At least three times as long as you think it could possibly take.
You think it's just one project? No, it's three or more. You'll uncover issues you didn't anticipate and/or you'll go into "while we're at it" mode.
As for those hatch covers that won't stay in place. The Velcro tabs and 1 inch diameter finger holes sound like a good low cost solution in lieu of replacing the missing cushions. You'll need three times as many as you think.
