Some problems after upgrade

[wither]

Hi all. I just upgraded from RC1.2 to RC3, and I am now having some theme issues. 

All input boxes are now blue instead of the original brown color, Ive searched through the varying .css and .php files trying to find the color to change it, but I cant seem to find it, perhaps someone could point me in the right direction?


Another issue is the appearance of an additional horizontal rule...


And the last issue is the linktree is no longer in one line, but in multiple lines one on top of the next...


Any help fixing these would be hugely appreciated.  The forum url is http://theaudacianrepublic.com/forum

[CapadY]

RC3 can't work with templates for RC1.2 so you have to make sure to have a RC3 compatible template or to have to make a lot of changes by yourself.

[wither]

Right, I figured that, which is why I went about fixing these issues myself.  I have already fixed a few of them, these are the only remaining issues, which I cant seem to find.  I can live with the extra horizontal rule and the linktree as they are, but the different colored boxes are annoying.  I just need to find where the color setting is for it, as I said, I cant find it in the stylesheet or the index.template.php, or any of those that can be edited via admin.  Which is why I posted here, I figured someone who knows what theyre doing would know where to find it and be able to tell me.  Perhaps not?