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Use sandpaper and a paint stur stick...start with 250 grit and end with 600. Primer should be the same product as the paint/clear coat. Its called a system.
250 grit untill you get to the old primer (don't sand through the gel coat)
Prime it
sand with 250 then 400 (wet)
Prime it again
sand it with 400 then 600 (wet)
shoot it with color
shoot it with clear while still wet with color
Let it dry wet sand it again with 1000 grit (wet)
Buff it out .
Being a some what flat surface you should not have much trouble.
Thanks, I may just strip the thing and let a local shop repaint it. I wonder what that would cost. Anyone got a feel for the cost of just painting a hard top only after I strip it?