You could extend the breather pipes, there are kits available to do so, though it is not rocket surgery, the problem is where ? I would think the rear axle could be taken up in to the rear pillar, and you would probably be ok, but this would require further investigation.
The problem as I see it would be the front ones, you could extent them to the bottom of the A pillar without to much worry, in effect top of bonnet height. Some off road vehicle owners like "GOJeep" have come up with alternative solutions for the air intake too.
http://www.go.jeep-xj.info/Exterior.htm - See Air intake diversion hose.
After that where too ? On Raised Air Intakes I fitted to other vehicles I would normally fit the breather tubes out side following the RAI or "Snorkel" up. So next question is where to get a snorkel ? :biggrin: