Sgt, it will get easier, and faster, although Greg Lemond once said "It never gets easier, you just get faster". So there is a balance between the two.

Assuming that your commute is mostly over paved roads, a mountain bike is not the best option for a bike, but it would work. Changing the tires from knobby ones to something with a smooth tread will increase your speed. The suspension in a mountain bike also sucks up energy which could be helping to move you forward, so a bike with no suspension is better for commuting than a mountain bike.

Your legs will get better with time - don't overdo it, and give them a rest from time to time, but I would expect the ride to be much more comfortable in a couple of weeks - you will feel better too. Have no idea about your question on how much you would lose by taking 9 months off - I never take more than a couple of days off the bike.