If you have the space at office to store extra clothes, you could take the train/drive one day in a week and store work clothes/shoes for that week so you have to carry less on the bicycle. For riding itself, I would recommend purchasing a jacket and shoe covers for rainy days. Also try doing the bike ride to office on a weekend to see if you can ride safely and find out amount of time it takes.

Cyclocross bicycle's geometry is usually different than that of a road bike's. CX bike also has a higher bottom bracket, cable routing on top tube is not on the bottom of top tube to be able to shoulder the bike.

If your road bike has brake lever with integrated shifters, this will take some getting used to.

If I understood your question correctly, you have flat pedals/flat pedals with toe-cages. I used full grain leather/ water proof work boots on flat pedals, it was tough to get them in the toe cages though. Just wax the boots weekly, they will keep your feet dry.