Getting a new bike is pointless. Especially since the resale value of carbon blows. You would be lucky to get a crappy low end 9-speed commuter with the money from the sale of this bike. Both my commuters are full carbon flat bar road bikes with a mix of ultegra and 105. I love them.

>I figure that something like Gatorskins is first.
Definitely a good idea to get tires with aramid/kevlar belts. They help but are no panacea.

>What about a new step and bars? straight bars?
Flat bars are IMO indispensable if you plan on riding extensively in traffic. If your stem is too low you should be able to flip it and buy a decent carbon fiber or alu flat bar ($20-100). You would also need new mountain bike levers ($10-50) and microshift/shimano flatbar shifters ($50-140 depending on brand and number of gears). Microshift shifters are 100% shimano and road component compatible.

>And pedals - I am thinking of speedplay Frogs (I have speedplay light action and then Shimano 105 road).
Road pedals are definitely annoying for utilitarian riding. Frogs or standard spd are great. I prefer spd because one can buy excellent wellgo ( ~300 gm same weight as XTR) pedals for $25-30. (Wellgo manufactures shimano's spd pedals.)

>So should I just get some platforms? Really aggressive platforms?
Forget the platforms. If you've learned how to use clipless there is really no point in ever going back.

>Or use my road shoes ($250 carbon shoes, carbon soul) with the Speeplays I have.I am worried about dismounting and walking over the train tracks and such.
Except for race-level shoes, mountain cleats are recessed. I have keen commuting shoes, keen commuting sandals, and shimano mountain bike shoes. They work great and I've walked a mile or two in my keens without much discomfort.

As far as fenders, I recommend SKS p35s since they are much less prone to bend and get caught. I've run p35s on tires as wide at 28 mm and unless you are riding on gravel or dirt I cannot imagine why you would want wider tires. P35s can also be made to fit most road bikes although you may be limited to 25s.