Are you looking to get rid of the seam altogether, or just the weather stripping? If just the stripping, you could likely use body panel adhesive or windshield sealant, smooth it out before it hardens, then paint it.
An Xterra style rack would help with the lines, so would an exo-cage, if a cage is in your long term plans.
I believe this was done by Marlin's shop 10-15yrs ago.
