Go straight to the window manufactures web site for proper installation.

Windows differ greatly between manufacturers but in any case caulking should only be considered a temporary seal and/or a cosmetic joint filler.

Okay, I found a pdf on the parent company's site that appears to be the right one. There have been some product changes, perhaps mainly name changes, since these windows were purchased.

With most of the interior trim, the drywall and the insulation removed, should I be able to see evidence from the inside of the metal sill pan referenced in the instructions? If the exterior brick sill trim is removed (to be replaced at a sharper angle) should I then be able to see evidence of the metal sill pan?

My guess is that the windows were not installed per manufacturer's instructions. I've only been able to see house wrap and tape, with the corners of the house wrap cut to permit it to be wrapped around the wood framing and attached on the inside.

The instructions also reference a structural engineering report for windows installed in high wind areas, but I could not locate it on the website. I plan to call the local supplier, and then the manufacturer, this week.

The question will be how you retrofit sill pans and flashings into a finished home. I must say that the "standard" installation here would just be house wrap and filling the void between the frame and structure completely with poly foam. Window flashings, let alone sill pans, are only just appearing on high end homes.

By following the mfgr's install requirements, you will keep your warranties intact. If they are not currently installed according to those requirements, which it sounds as if they aren't, you wont have any valid claims. Best bet to stick to those mfgr's specs and have thewm installed accordingly. Some window mfgr's will send out a rep for advise but in any event, keep in close contact with the mfgr.

"The question will be how you retrofit sill pans and flashings into a finished home." You've hit the nail squarely on its head, Worthy. One house in this neighborhood that had all of its brick, stone and stucco removed several years ago (different builder.) It boggles the mind to contemplate how much that must have cost.

Sierraeast, the problem is that the builder of this high-end spec house may not have followed the mfgr's installation instructions. I cannot be certain at this point. The builder now says he will ask a mfgr rep to look at the windows, so I hope a solution is found soon.

We had problems in a previous house (different window co.) and the local authorized dealer/installer paid over three dozen visits to our home as we tried to work through those issues. I don't think I can survive another such experience with my sanity intact.

Until recently window manufacturers wanted nothing to do with installation details or recommendations. Now they each have their own instructions, some good and some bad, and they differ between various models with no apparent logic.

A window manufacturer's warranty is usually not based on performance but is limited to "manufacturing defects": 20 years for the glass seal and 5 or 10 years for the non-glass portions of the window. Poor installation can void the warranty but only for those issues directly caused by poor installation. In reality what poor installation does to a warranty claim for a less than obvious manufacturing defect is muddy the water and weaken your claim but it cannot absolve a manufacturer from responsibility for provable manufacturing defects.

Usually a contractor is not obligated to install a window according to the manufacturer's instructions unless those instructions are referenced or included in the construction contract so looking up the current recommendations is usually pointless. There are many installation recommendations that I would consider completely inappropriate and many contradict the recommendations of the air/weather barrier manufacturer. They also change without notice so it is hard to prove what was in effect when the contract was signed.

This dispute is between you and the builder since he owes you a house that doesn't leak but how to achieve that is a negotiation between the two of you. A window rep might be helpful but many have no idea how to fix a problem without removing the window unit. The best way to resolve it is to get an independent waterproofing or design professional to offer a solution for your specific situation. That professional should work directly for you.

You said "windows". This is not something to let slide. I second MA's advice.