Freddy, from the photos it looks like there is no quick and easy solution. I can see a lot of evidence of quick and easy fixes. There isn't one thing I can see that was installed properly from placement of vents, lack of vent, wall flashings, use of exposed roof cement, shingles on to low of a slope...
My suggestion would be to find a reputable roofing contractor who can provide you with proper materials, flashings and expertise to have a functional roof system.
The biggest thing we see in premature roof failures is not failure of roofing materials but the misapplication of the materials. Time to start over from square one on this one. Wish I had better advise.
And remember the best value in not the cheapest price.