Iframes are very bad for SEO, amoung other things.
XF is very easy to customize so that it looks like the rest of you site. For example I'm using XF, X-Cart, and a few custom coded systems and it's very hard to tell that they're all complete different systems.
Do you have a link to your current site? Feel free to send it via PM.
no joke and not being cynical in the least bit...you can make the header area including navigation and breadcrumbs look like anything you want given that you want to take the time to do it right and have or are willing to acquire some html and css skills.
I can help you some but not without seeing anything so feel free to msg me when that time comes