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In another post i mentioned that my home had been vinyl sided over the aluminum, but right now I have some water running down in between the vinyl and aluminum, Do I need to Caulk the flashing,to the roof ??

A better or maybe more pics would help, but from what I see, you may have more than a caulking problem. That looks like rolled comp roofing pulled back and roofing nails in your roof. From the pic, this also looks like a big ponding area. Also further down the roof, it looks like it is ponding there too.

Rolled roofing, even torchdown, will not survive ponding very long. Nails on top of the roof and those holding on to that trim will leak regardless of ponding. But if the nail is in a ponding area, it will leak until it runs out of water.

Caulking may be a temporary repair, but you may need to look into a longer lasting fix.

Most times you can fix ponding areas by repairing trusses, but sometimes it is just loose metal between trusses. Sometimes you can go through the ceiling to block between the trusses with 1x2, to keep the metal from concaving in like that.

A sure fix is a new metal panel roof like the ones mentioned here at this web site often. This is the one in Mark's Mobile/Manufactured Home Repair Manual. There are also insulated aluminum panel roofs like the product I sell.

Your roof, or at least the part in the picture, definitely looks like it is at the end of it's life or at least in need of some major rehab. I personally would look into either installing a peeked roof or major repairs prior to redoing the existing roof if you plan on staying very long.