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We tried finding ways (a long time ago) of bending the code in such a way that the main content appeared first in the source, with other parts of the code appearing later.
A tough task ... and one we never came close to acheiving! With HTML being a code of structure, it actually made sense that bending it in such a way wouldn't be possible, but it was worth a try.
I don't know if there is now a way, particularly with CSS, to do this.
If not possible, then I would suggest simply looking at your 2 includes to make them as cleanly coded as possible, eliminating all reasons for spiders being forced to leave i.e. broken code, un-needed lengthy code etc.
We did a similar excersise recently on a site that had both a header and left nav include appearing before the main content. The includes had been written be an ex employee. We managed to chop over 100 lines out of the code and still have it working the same. (it had been very messy!)
Hope this helps.