-If you're running a lot and have an ipod nano, think about investing in the Nike+ system. It might sound like a bit of a gimmick, but there is a reason people use expensive pedometers - they're great motivational tools. If you don't have an Ipod Nano, there is another option, but it throws an extra $50 or so onto an already sort of expensive investment.
-Directly related to that is get good shoes. It's pretty tempting to skimp out on running shoes, but they're actually pretty important. You don't want shin splints, trust me. You don't have to go huge, but a decent shoe with good sole support is key. Also, if you're running longer distances than you have before you might have to retrain yourself a bit to strike with your heel instead of your toe.
-Going to the gym blows, but you can make it better. Bring an mp3 player with both music and podcasts. I personally go at around the same time every day, but that's mainly because I have to. With an erratic schedule the main thing is just to make sure you go the days you need to go. Figure out how many days a week you have to go and figure out a rotation schedule around that. If you have to skip a day for whatever reason, make sure you make it up the very next day and then alter your schedule around that. The main thing I find is to not give yourself the option out and just kind of turn into a robot. You're also not getting body-builder jacked so you don't need to spend any more than 40 min. in there.
-The best way I ever did it was go to the gym for a little in the morning, go to work, go back to the gym for a little after work, and then run after on nights I'd do cardio. It sounds like a lot, but worked out to be less of a time investment then if I just went to the gym once...it was also a hell of a lot less boring. It is a bit of a bitch to pull off though and might have some kind of negative effect on your results, I don't really know much about the science behind it.
-There are all kinds of 'web 2.0' sites out there that will help you keep track of shit. I don't know any by name but I'm sure I can find some for you.