Re: help with custom theme breakage
Looking at your layout shows some critical issues. You describe an element twice and give it the ID #container. ID’s are unique tokens that are only allowed to be used once per page and as such are generally applied to major markup framework structures #container is one such framework element that generally would occur once along with IDs such as #wrapper. It is an error for it to be used twice and that needs to be addressed first. If that element really does need to appear as a parent of #content you could change it to a class but better is to rename it altogether (second occurrence) However neither of these elements appear to have any rules associated with them so I wonder if things are not getting slightly mixed up here?
#content has the property clear:both this will (and does) have the effect of clearing any previous floated elements or columns and is why it positions itself below what appear to be your sidebars, also it’s full width; in a basic three column layout you would need to add margins left and right equal to the sidebar widths doing both these things will pull that #content area up to the top, but the right sidebar will remain cleared below as it’s a floated element and follows after non floated content and must drop to the next available line and would require source ordering tricks to enable it to take position alongside #content.
tbh at this stage I would be suggesting that you step back and revert to the previous styles as this feels as though it’s got a little out of hand and it’s difficult to correct in it’s present state. Start afresh and work through changes carefully perhaps seeking advice as you go. One of the difficulties is that without knowing for sure what the layout is supposed to look like or looked like before and what actual changes have been effected it’s hard to offer advice.