Run, bike, or car. I figure a combination of the 3. If the course was a 26.2 mile straight line with all the cross roads being laid out in a simple grid without any tricky things like railroads, lakes, mountains, crowds of spectators...then a single bike or single car could get you around to each checkpoint with minimal difficulty.
If he got around by bike then he'd have to stash it at say mile 3.2. Run the first 5k at sub-3 pace (not difficult), hop off the course, get the bike, pedal to 6.3, get off, back track on foot, get back on the course, cross the 10k mat at the right time, hop back off the course, get to the bike, and repeat. But you'll hit a snag at the 15k with there being big lakes on both sides of the course. Looking at google maps of the area it still seems doable, but you'd have to leave the bike on Pond Street and run a loop around Fisk Pond.
Now a few more snags with biking for the 20k. First, you can't dump the bike at 12.5 circle back and have time to redo the stunt and hit the mat at 13.1. Second, there isn't a good parallel running road between Natick and Wellesley. And finally, getting on/off the course in the area around Wellesley College is going to be the most difficult section off the whole course with the psychotic slutty spectators.
I'm thinking the way he got from the 15k to the half was by running. We know he didn't run the rest of the way straight to the finish because he would've lost time changing clothes, so if he did it alone then he would just need another bike stashed somewhere shortly after 13.1. Then he could keep doing the bike thing up to the 35k, and at some point change clothes in a car.
If he was alone then driving doesn't seem likely. It would work great early on, but no chance after Newton. Driving around Boston is TERRIBLE on a normal day. On Marathon Monday with road closures, and out-of-town spectators driving around the city...there's just no way. Way too risky. You'd never be able to drive a few miles, find parking, and get to the timing mat in time. And suppose he used a car the first 15k then biked after the half. He'd have to bike back to his car after the race and have a less convenient place to change clothes. Going into a hotel to change race clothes is risking too many witnesses.
I just ran Boston on Monday and have been thinking about how anybody could've cheated this race for a while, and all I can come up with is that he either used a couple bikes or he had help.