Explorer has modified the Dodge roof gutters in the front and rear and these areas become problem areas before the rest of the roof gutters cause closer inspection and reveal the fiberglass has been hiding a worse rust issue for quite some time
Originally roof gutters were sealed with a seam sealer which remains somewhat soft.
The silicone was likely a much later attempt to seal the zone where fiberglass meets metal.
Is there a bunch of rust in the roof gutter?
The 2 part seam sealer of choice by collision chops is a 3m product. the 1 part seam sealer products are no good according to reports.
http://3mcollision.com/products/sealantsIf there is rust, which is likely, get some Ospho and treat it as best as possible. Paint or other products adhere very well to a surface treated with Ospho when directions are followed.
While it might appear you have removed all silicone, it likely is still there microscopically and will repel all attempts to adhere more sealant/ adhesive to it.
A Scrubbie pad and Ospho can remove it for secondary bonding. the Oshpo did not hurt my painted surfaces, unless I let is stay on the paint for a while without wiping it off. Even then it just turned oyster white paint a lighter shade of white.
I've spent way too much time on my roof gutters, all because I halfassed it originally, and because the conversion company originally decided regular drywall screws were perfectly acceptable, may they rot in hades.