Hello florida hybrid. Glad you decided to use your bike to get back into shape. It's a great, low impact way for us 40 somethings to get started!
As for pedals and shorts, experiment and see what you like. I would estimate about 10% of the "upgrades" I add to cycling wind up being a loser, but experimentation is part of the fun.
I only ride about five miles a day on my commute, but I do it in full lycra. I don't care how I look, or what people think. It's more comfortable for me. I put clipless pedals on my new folding bike after a ride in the rain, when I kept slipping off the platform pedals.
Check the laws pertaining to bicycling in your state. No sense getting hurt. The Advocacy and Safety sub-forum has good advice, if you can cut through the...uh... emotion that springs up from time to time.
I think Loooty has the best advice: ...cycling can be taken far too seriously...don't forget to have fun.