If you have any money still outstanding you might be able to use it to get them to put up the proper flashing. That has to be done right to be waterproof. Flashing around roof extrusions (dormers, vent pipes, etc.) should be part of their job. They probably underestimated the job and don't want to put anymore money into it, but that's not your fault.

The job's not over until you pay. Have you paid? If not, you have a whole lot more leverage.

You need the siding replaced so it covers the step flashing. The workers did step flashing as it would normally be done in anticipation of siding.
If you do not plan or residing any time soon, you could ask them to add a strip of flashing overlapping the step flashing and running under the siding. It could then be painted to match, but it will still not be very attractive, but at least it would keep water out, which it will not do as-is.
Casey

What I run into with the few jobs we've had to have contractors in for, is that they know exactly what the finished product is going to look like and sometimes I don't know enough about what their job is, to even ask informed questions. Uhm, that's why we hired them. LOL.

I also have had contractors make decisions when they run into snags or unforseen circumstances. Some will come knock you up and ask your preference, and some will just do what they want and then when you see it, and are displeased, they basically tell you they'd have to rip up the whole job and redo it to do it your way.

So, I really understand why you are upset......because in essence it still needs work on it no matter how you cut it and if they didn't know whether you were going to repair the siding, they could have asked.

But, I also think Casey is right. There is no way, short of them being siding installers to fix this in an attractive manner. But, no way should any roofer leave a roof in a state where it isn't even watertight without at least contacting you and warning you. At best they had to know you'd be calling them and seeing red. At worse they had to know that eventually you would have water damage, and were they hoping you'd not know for a long, long time?

I think I'd be more worried about what is now 5(!) layers of roofing than the siding/flashing issue. I can't imagine any state or local building code that permits this many re-shinglings without stripping off some of the old. There's a serious weight issue and unless they used the equivalent of 8 penny nails on the latest layer, there's a real question about how well attached this layer could be. Further,your warranty from the manufacturer of the shingles is almost certainly voided by this installation.

Thanks for all the really great replies!! Maingrower - it was a complete tear off, sorry I didn't make that clear. Everyone else, yes, it looks unattractive, but we've discovered it's as a few of you were guessing - it's proper and water tight. I've been stressed and swamped the last few days and my parents are here as well, so I apologize for not getting back sooner. Our neighbors (both experienced in the trades), 1 of which was actually home during parts of the install both say they did a good and proper job. So I am content as far as that goes.

Now, as far as them dinging up the houses on both sides due to serious carelessness, that's another story, but the roofer is working it out to their satisfaction. Basically the protection they put up on each side during the tear off came down before they were done tearing off.

And then there's the electric on a small portion of the front of the house (2 lights and 2 outlets) that has suddenly stopped working. I think the wires were run through the ceiling in that area, which is right under the roof. No crawl, likely no insulation. There's a licensed/bonded electrician they are sending out next week to take care of that. And some other minor stuff also being taken care of.

And no, we will not be paying them until everything is 100%. Sigh. Why does it have to be so difficult?

did you check your fuse box/ circuit breaker? I'd either remove the appropriate fuse or throw that breaker. Something has disrupted electical flow, and until an electrician checks it out, have you thought of cutting the power to those wires?

Thanks Scott! DH did check the fuse box, but still nothing. I will ask if he pulled those (that?) fuse, that is a REALLY good point.