If your roof is EPDM, your leaks are most likely at the points where there were holes cut in the membrane: vents, antenna, etc. That is, IF the membrane has been cleaned and treated as it is supposed to be. Also, depending how the sides, front and rear seams are attached, that could be a source of leaks as well. Dicor Corp., who makes rubber roof material, also makes a two-step roof coating that you could use if you are convinced that the membrane has become porous. Replacing the roof is an option, but you are talking thousands of dollars. There's a permanent waterproofing tape called "Eternabond" if you decide to go after the seams. A couple of years ago, I bought enough to seal all the vents, antenna front, rear and side seams. (my rig is a 2005 Cardinal Platinum) It cost about $200.00 for the tape. The 4-inch width works great. My rig is the same age as yours, and my roof is still in great shape, but I maintain it faithfully twice a year, every spring and fall.
I hope that this doesn't make things more confusing!
2005 Cardinal Platinum 35 CKT
1999 Dodge Ram 3500 CTD Dually Crewcab with Lots of Mods.