1) It seems to be better suited to a larger screen. I had to zoom it out a bit when viewing. The main page doesn't even fit on my laptop screen (1366x768 pixels). The menu is cut off at the bottom of the screen.
We did design the site for larger screens (1280 x XXX) but it should look okay on (1024 x 960) as well. We are working to make sure it looks okay on an iPads and tablets.
As you mentioned, the width on my screen is fine. The problem I have is that more and more screens are going to a "true HD" pixel ratio (16:9). So, my 1366pixel wide screen is only 768pixels tall. That's almost 200pixels shy of the minimum standard you mentioned (1024 x 960). Just something to consider. I've done a little web design in the past, and I certainly realize that it can be difficult to plan for EVERY hardware configuration... not to mention the browser and screen layout that every user is using.
1) It would be cool if you could select more than one spec to be used to build the list of results (for instance if I wanted to see all rosewood bodied, GS guits, etc).
The reason you can only choose 1 filter (Shape, Wood, Series or Category) at a time is that it ensures there will always be at least one guitar in the results. If we allowed 2 filters (for example, a shape AND a wood) it would often return no results which is very frustrating to users. So we did the next best thing which is a sort of the results.
I can ONLY speak for myself here, but I would have to say that I would prefer to see a set of empty results, or some message that says that Taylor does not currently build a guitar that meets the filter criteria that I've specified (then maybe point to the BTO page?). Otherwise, I might spin my wheels for a long period of time searching for something that really isn't there. However, if I wanted to search for, say an Acoustic GS, I could do that. Right now this cannot be done, and if I search for GS body shape, I have to sift though pages of xxxCE guitars in order to view the GS3 through GS8 models.
2) I wish, when displaying the lists of results, they could have a selectable format (like small icons). This could allow many more guitars to be displayed on a single screen. There would be less pages to of results to click through.
Would allowing you to select the number of guitars to show per page work? For example a dropdown with 9,12,15,18,21 options?
I think this would be a reasonable compromise, since I'm sure my suggestion would be more involved to implement. However, going back to my short screen height, this leads to a lot of scrolling that smaller images would reduce (maybe I just lazy!). But then again, multiple filters might also reduce the number of search results.

Thanks again for the great opportunity share our opinions!!
