I have raced triathlon and MNT Bikes for years, and I am currently in the military so I have done my fair share of forced marches with a heavy ruck. If you are going to be carrying a lot of gear and may need to make it farther than 50 miles total, I would approach them the same way. Ride for about 50 minutes and rest for about 10. This will keep you going over the long haul.
A few thoughts on components and misc cycling equipment. If there is any possibility that you are going to be off road, a road bike will simply not due. Maybe a cyclocross, but unless you are racing cyclocross, why spend the money on that kind of bike. If you are looking for all around fitness, and real possibility as a BOK, I would get a decent MNT bike and two sets of wheels. One with slicks and one with knobby. Train on pavement with the slicks, and if the time comes, you can switch easily and while the knobby tires are more resistence, they allow you to ride pavement or off road.
Cycling shoes: You are definately not going to want to ride any kind of long distance without having your feet attached to the petals. Especially if you are looking at using this as a form of exercise as well. If you get mnt. bike petals and clipless shoes, you will be able to walk fine for short periods (i.e. scrambling up slopes) and you can just carry your hiking boots with you if the need to abandon the bike arrises. Even using boots with clips is not a good idea for long periods of time. The real key to cycling shoes is that they have a stiff sole. This means that all of the force that you are applying to the pedals is actually being used to drive the bike forward. With flexible shoes, you are not only going to lose energy with each stroke, but you may also get sore soles of your feet.
Groupo: If you feel the need to get a higher end groupo, 99% of people will be well suited with Shimano Ultegra and it will save you a bundle over the other higher end groupos, and you will not notice the difference unless you have been riding a long time.
Handlebars: you are definately going to want bar ends for a ride this long on a mnt. bike. These are short peices of pipe that attach to the end of your straight mnt bike bar. It not only gives you an additional hand grip, but I often rest my forearms near my elbows at the corner of the bars for a more relaxed position. However, if you are not used to aerobars or riding in a low position you may not find this as comfortable as I do.
Suspension: On mnt bikes, you have three options for suspension. No suspension, front shocks, and front and rear shocks. The full suspension is really designed for down hill racing, where absorbing shock is critical. If you are riding a long distance off road, you will probably appreciate the front suspension, but if you are trying to mount a front rack for equipment, you may find that this causes problems. Just another thing to consider.
Final note, be careful about going to a bike shop as they are often more interested in selling you something you may not need then really giving you what you are looking for. Not all are this way, but as I learned more about cycling, I learned more and more that the local shops were trying to rip me off. YMMV.
Bottom line, find what works for you and your intended purpose and go with it. But I would definately get out and ride, if you are considering this as a means of transportation.
Smackdaddyj