My shingles have a ripple/raised effect all over. I'm not sure if the shingles need to settle or what. And they didn't install flashing along the 2nd story walls where the shingles butt up against the house. This left about a 1 inch perpendicular gap between shingle and where the siding begins. There is also a lot of shingle pieces in cut half to make, what appears to me to make a complete shingle. This is not everywhere, just in one section of my house. My thought is they were running low on materials. This worries me with the cuts in the shingles because of leakage, but I'm not an expert. The gabel vent seems to ripple/wave along my ridge like a ridge of an old 17th century house. Compared to my neighbors roof replacement from 2 weeks ago, mine looks horrible.

You call the company to come back and fix the problems, if they don't, you get a couple other companies to give you a written estimate to fix the problems and sue the company that did this

Or may I assume you have not paid them for all of the work yet ?

This sounds like a very shoddy job and I would not settle for anything short of a total replacement. If they won't do that hire an inspector to make a report, take pics and sue them.

No I have not. The sad thing is I did my research (BBB etc) and these guys were recommended by Gaf Elk with a lifetime warranty on material and labor.

well first most roof warranty have so many "ifs" don't actually expect to collect on it, it is the manufactors warranty, which does not cover hail or wind over the rated amount.
Plus if the shingles do not have the approved number of nails, the wind warranty is voided also. ( can't remember if it was 6 nails per shingle, but normally more than most roofers actually use) And of course things like the rubber boots, and metal flashings are not covered normally in the warranties.

But don't feel too bad, we just had a roofing company, that did 1000's of great jobs, and a high BBB rating, just close, they sold roofs the last 6 weeks, and did not do any of the jobs, ( 100s of jobs all with high deposits)
Some people who got their roofs found out the shingles were never paid for and now the lumber yard is putting liens on the homes for the value of the shingles.

There are more fraud in roofing than almost any other home improvement area.