"What type of roof would this 2004 unit have. What should i do to maintain it?? Any help would be great."
You may have a rubber membrane roof, take a look up there and if it feels rubbery, well, yes. There are threads and threads on roof care but they seem to boil down to cleaning with a mild detergent like Top Job or Spic and Span, use a soft brush and be sure to rinse thoroughly after cleaning.
Here is one of the threads care and maintenance for your rubber roof
"Also have problem with back window. looks like all trip is dry rotted and someone tried to silicone around the window but still I see water on inside window frame when a hard rain comes. Any ideas who or how to fix."
If it is like my rear window, an automotive glass shop might be able to help out. They have the expertise to seal things. Post a photo so we can be sure.
"Also any one have leaking issue on roof up front over cab where the seam is going across bunk area. mine has some damage and looks like some one tryed a bubba fix. I put eternabond but not sure how good or long its gonna last before i should have professionally fixed."
Did you "prime" the surface where you put the Eternabond by wiping with Acetone or the suggested cleaner? That would remove dirt and such and give you a good sealing surface. Herk would be a good one to ask.
Chris in Virginia