You should definitely go with some sort of bike short. They are padded in the crotch and that can help make or break your evacuation. Saddle soreness is no joke, especially if your well being/transportation depend on you being able to go. And no, standing up for miles on end is not an option. This is also why you need to get out and ride the thing on a regular basis. Even mild off road trails/dirt roads will beat your butt harder than Bubba the lonely 300# cell pimp.
One thing that hasn't been mentioned yet is bike shoes. Just like you shouldn't skimp on hiking boots, the same goes for your riding shoes. The cheap ones won't be secure, durable, or stiff enough for good riding. You don't need to drop $250 on a pair, but avoid the $50 (regular price) versions like the plague. That said, riding shoes are not hiking boots and vice-versa. You certainly can get away with a set of toe clips and hiking boots, but if you learn to use a good set of clipless pedals and riding shoes you'll be much happier. DO NOT go bare pedal. Get a set of clipless pedals and shoes to match or use the toe clips & straps with your hiking boots, plain pedals will have you falling on your head faster than you can imagine.
Tailor your tires & pressure to the terrain you're going to be riding. You can easily get away with less aggressive, higher pressure tires on dirt roads, but real knobbies on pavement/easy dirt trails/roads will be a waste of energy just like a set of slicks will kill you on real trails.
Use motocross gloves, protection, dexterity and thin in the palms, enough said.
Thick padded grips will cause you more problems than the thinner less padded versions, you won't have to grip as hard.
Get a CamelBak or something similar. Much easier to use than water bottles and the water is on you instead of the bike should the bike become a non-option.
Keep you body and your bike in tune. A rusted out drive train will ruin your plans just like a 55" beer gut.
Ride your route so you know what to expect, how to get where you're going and possibly stash items you don't want to carry all the way (food, water, ammo, etc).