I haven't been to the Holy Land but in my travels to the Middle East, I've learned that all of those customs you read about (such as the soles of your feet you mentioned) are just for playing it safe. In Iraq, you had the holiest of the holy in some areas and drunken orgies in others. Just stay on your toes, be respectful and courteous even if others seem to slack in that regard, and just be alert. No place is absolutely safe but as long as you apply common sense, you'll probably be OK from the way you talk of the place.
Good luck. Get your business done and get your tail home.