I'd highly encourage getting some clip-in pedals. Don't mess around with the road-style pedals, just get some Shimano SPD (mountain bike-style) pedals and some MTB shoes; you'll then be able to walk around normally when off the bike and have proper control at stop lights during your commute.
I find that having my feet clipped in allows far better control of the bike. It also saves a bit of energy, not because I pull up on the upstroke but simply because my foot is always in the optimal position. Also, a real pair of bike shoes will probably have a stiffer sole than what you might be using now, allowing a better transfer of energy.
As said by others above, it sounds like you've already got a lot of good base miles in. I would just do some longer (40-70 miles) weekend rides to figure out what food and drink works for you. This doesn't need to be fancy sports drinks and foods, some people do just fine with regular food and stuff found at gas stations.
Regarding the bike, a road bike modified for commuting sounds pretty good for a long distance machine, you may not need to change much. For the gearing, you'll have to have an idea of what the route is like to know whether what you have will suffice. Bear in mind that a small hill 90 miles into the ride may feel like a major mountain by the time you get there.