There is no way I would have the builder reinstall the windows, especially since they are already flashed. The Andersen 400s I've seen have an integral vinyl flange to the cladding. To tear off the flashing and pry up the flange would leave a mangled mess, and probably leave you worse off than before. The merits of the caulking are debateable with proper flashing. I would sleep just fine at night knowing the windows are flashed properly.

Update: The guy took up the toilet, removed and relaid some of the uneven floor tiles (still uneven, but now not directly under the toilet) and installed the new toilet I bought. He agreed to pay for the toilet ($350, not counting the seat, though one just like the one he broke was over $500), and said he would consider whether it was feasible to remove the deco tiles and a couple of rows above and below them, and put them back properly. The tile dealer offered to sell him the replacement tiles at her cost because she felt bad about recommending him. That was over a month ago, and I have not seen or heard from the jerk. I'm guessing he has no intention of reimbursing me for the broken toilet or rectifying the bad tile job. I don't think I want him back here, to be honest. One of the floor tiles came loose, and I had to pay someone else to replace it, doing the best they could with the uneven adjacent tiles. I had another tile contractor come in and price the removal and replacement of all of the tile from the deco row down to the tub. He said the tile was crooked, caulk line at the tub was way too wide, decos done badly, and all of this was prefaced by saying he doesn't like to criticize another contractor's work, so I'm thinking he was holding back a bit. I've already bought the replacement tiles (at cost) and I'm waiting for the second guy to get me on his schedule. The cost to correct the first guy's work as much as possible will exceed $1500 by the time we're done, and I'll still have uneven floor tiles and a slightly bellied back wall in the tub area. I've since learned that there are so many people looking for this guy that he took his name off his truck. He has also reportedly stiffed a local building supply company for a lot of money, and his licenses for remodeling and building are both lapsed for over a year. Live and learn. Maybe my loss on this project will save someone else from going through a similar experience. I live on the CT shoreline, if anyone is interested in the name of the idiot who did this, contact me and I'll give you his name.

Mmm, I had my chimney reflashed this year and it was about 200 dollars (that included sealing and fixing a couple bricks) it has a warranty for five years I think. anyways, won't the new chimney have flashing? Then it will fail in about 3-5 years and you will have to get new flashing again also, regardless if it is new or an old chimney. So Eventually I think that it will look ugly, like the older chimney. also you have an old house and old house owners know it isn't as easy as you think (nor as cheap) if you tear down the top of the chimney I bet you will find other things that need to be repaired and the cost and time will increase! If it were me I would go with just the flashing repair. We had tar all over the chimney also so the repair was done with some sort of epoxy or something. It looks black but isn't tar. Anyways, the chimney looks SO much better now. I think they cleaned up the tar a little while they were up there. Because of the degradation of the chimney bricks, which were then tared over, it would be difficult to put the metal flashing on our chimney. Also the bricks are very rough. Our house is over 150 yrs old also. Our chimney is not used anymore though. We use the front chimney and we have a liner in that.

If there are two flue tiles sticking out of the chimney top, I can't think of any way the chimney would not have two fully lined flues. There would be no way to support tiles just at the top and you would not have two separarte flues to accomodate the furnace and fireplace. What kind of condition the flue tiles are in is another question entirely. 6" under the shingles is not really very much at all, so water could indeed be running under and back toward the chimney, especially since the roof itself is "swayed". A second factor is the age of the roof. Unless they are very heavy duty, 22 years is about the life expectancy of asphalt shingles. You really have two different if related issues: the condition of the roof itself and the condition of the chimney. Some chimney sweeps have video cameras they can lower down the chimney to check the interior. A roofing company can inspect the total roof. Potential expenses for sure, but continuing to try and deal unsuccessfully with the leakage is not a great option either.