The Marathon Plus for MTB's,
http://www.wiggle.co.uk/schwalbe-marathon-original-greenguard-rigid-mtb-city-tyre/
http://www.wiggle.co.uk/schwalbe-marathon-original-greenguard-rigid-mtb-city-tyre/
1.75s will be fine, and on offer..
http://www.planet-x-bikes.co.uk/i/q/TYSCMARPPW/schwalbe_marathon_plus_performance_wired_tyre
make sure you get a good pump as well to get the pressure right it can double as a track pump and you can stick it on the bike/ rucksack, i like the road version of this ..
http://www.topeak.com/products/Pumps/MountainMorph
Chr15 all suggestions have been good, hope the pain lessens for you quickly. The fact that it'll lessen is a fact, just how quickly it happens for you
14 miles is a good commute length - but probably not when you're just starting out, so your plan of alternative days might not be too bad to give our knees/thighs a rest until you're up to speed. Once you are though, you'll love it. I often lengthen mine to 13 miles as I think it's the perfect balanced length for a commute.
Lastly, on the knees front, there really are two main ways to try and cure them (I used to suffer too)
1. Check the seat height again. If you can put it any higher, do so. Aim that when sitting on the seat, you can only just touch the floor with both toes as a rough guide, and feel more comfortable balancing on one leg. Its amazing the difference sitting higher makes to your knees.
2. Learn to really use your gears. When going uphill, for now avoid getting out of the saddle and attacking, instead stay seated and keep changing down until you can pedal easily. This will have the effect of making your legs spin a lot faster, but spinning faster is actually easier on the knees than pedalling slower and harder.
Keep it up, and good luck!