Thanks very much to all who replied to the original post, I appreciate the input and advice.
Contractor has been responsive, acknowledges the problems and assures me they will come out and replace stained shingles as well as remove and replace the poorly aligned shingles above my porch.
Questions: How would you guys remove the stained shingles? Do you rip out the shingles leaving nails in place then pound nails into sheathing and reshingle? What should I watch out for when they do this? I definitely want stained shingles replaced as per my communication with you guys as well as phone advice from an Owens Corning rep.
As far as the the crooked courses above my porch at the ridge, will removing this area do more harm than good? Can it truly be torn off and not damage surrounding shingles, underlayment, etc? I’m tempted to leave it as is since it’s just a cosmetic issue. I will probably never sell this house so inspection by a prospective buyer will most likely never be an issue. I just want the dhamn roof to last and not leak! Thanks for your time.