Right now the Twitter Bootstrap code has the header image sized to <img src="/images/headers/r1d6header.png" alt="r1d6header" width="1114" height="85" style="display: block; margin-left: auto; margin-right: auto;" data-pin-nopin="true"> I wouldn't worry about trying to make the image look better right now. Once you have the blue background removed, I can take a look at the source and resize the image appropriately and send it to you. It should look a lot better after that.
Well, the biggest problem I have is actually getting rid of the blue background up there. The T3 framework is a bear to make modifications to. I have a custom module position added to it that displays the logo, But it seems to be inheriting the color from the header code somewhere, and I have not been able to locate the piece that is causing it to inherit the site background color for the header section. I wanted the logo to actually appear before that, but can't get it to stop inheriting it. It is actually the module position that has that background and not the logo itself, so hopefully I can get that worked out, but it may take a few days. Took me 2 days to even get that logo position to work. The stock logo for the site it a tiny image in the upper left of the menu.
Managed to get the logo set up below the menu, I think that works ok. Could use a 2nd opinion on it though. I have it set static at 1280X100 right now, would do dynamic, but it would take 100% of the screen and stretch out. So if you can do one at 1280X something around 100, that would be perfect and I can replace the one that is there now. Cannot go any smaller than that, otherwise it looks weird..
Give me your honest opinion on how it looks now with the logo below the menu, it is a real pain to get it above the menu without inheriting the color schemes.
I think you will have less heartburn if you leave it a static size. I think Having the logo where you have it is fine, most Bootstrap based websites are like that anyway. I resized the image, so it should look a lot better.