There's quite some debate over whether clipless pedals don't make you faster at all, or make you slightly faster or more efficient. Either way though, there's no way it's worth it for a 4 mile commute. You'd spend more time changing shoes than any time you'd save on the commute. Toe cages don't make you faster at all, they just keep your foot from slipping off the pedal, personally I think they're kinda dangerous as it's much harder to get out in an emergency. The toe cages racers actually used were different than the what you see people using riding, I don't want to go into it but let's just say that there's a reason clipless has entirely replaced the old system in racing.

These are the top 3 reasons why people are slow on their bike from when I was in college:

1. They weren't inflating their tires. With skinny tires you pretty much need to bring them back to their regular pressure every day, with fatter tires every few days.

2. Their seat is to low. A lot of times people put their seat at a comfortable height that was less than efficient. If their seat won't go to a height that's correct and fairly even with the handlebars, then their frame is the wrong size.

3. Their brakes are rubbing. To test this you pick one end of the bike off the ground and give the wheel a hard spin (in a direction that does not cause the pedals to turn). With a hard spin it should rotate at least 5 times, if it comes to a stop after 1-2 rotations there's something wrong, usually the brake pad is rubbing.

Other things after checking those things:

4. If you have particularly bad shoes or pedals for biking.

5. If your tires are knobby, slicks are definitely better.

6. Higher quality tires can make you a little faster. So can skinnier tires (to a point), but I'd be hesitant to put skinnier tires on a bike that came with 35c's as they'll make the ride worse. I mean downsizing 2" tires is an easy call.