I don't know that there's a correct answer for when to go clipless. You will be more efficient and you should learn to be smoother in very little time after going clipless. It's for you to decide though, just as it's for you to decide what type of clipless system will work best for you.

Almost the same with shorts, but I will step out of line (with some people) and say that you will almost certainly feel like you can ride longer distances with greater comfort in proper shorts. I recently sent a buddy a pair of baggies with chamois, and he's riding a crappy mountain bike. He was skeptical, and then after the first ride with them he called me to thank me.

I would suggest that you go with a pedal that uses SPD on one side and is platform on the other. This will allow you to use a shoe that is comfortable to walk in or allow you to just get on and ride if you don't have much time.

Enjoy your Sirrus, I think it's a nice bike. I wish the one we have hanging in the stairwell was a size larger...we bought it for my son, who put maybe 300 miles on it, then my daughter put maybe 300 miles on it, now they both have road bikes and the Sirrus is a size to small for me or I'd use it for a commuter bike.