I had the same problem and painted it with lots of layer of RP ground and color. Than added protection tape. This all last 1 year (excesive offroad in heat in africa).
Than i just painted the area where the top touches the roof with 2 layers of rhino (something similar i got in south africa)
This now is perfect and will last forever i guess
2001 SMB E350 4x4 7.3 Powerstroke
1968 Pontiac Firebird 400 Convertible ,1978 Peugeot 504 Convertible,1988 Porsche 911 Carrera 3.2,KTM 300 EXC,BMW G/S Paris Dakar,BMW "Diabolo"