Actually now that you mention the emperor (w/bio-wheel) it makes a world of difference. Most the bacteria you need will be on the bio-wheel so throwing away the filter media won't make too much of a diff. Personally I'd keep it there as it may provide more places for the bacteria to colonize. The more oxygen rich places you have for colonization the faster it should cycle. Thats all and done for I guess but still shouldn't make too much of a difference if any at all. Just don't do anything to the bio-wheel!! lol
Cleaning the gravel won't do anything towards the negative. That is unless you have super deep gravel with stagnant air thats been trapped for a while and you decide you're going to stir it up.
You can scrub off the algae or not it doesn't make a difference to you cycle. Now knowing that you have the bio-wheel you probably didn't do too much to effect the cycle.
Just to let you know you probably could leave the filter pad in there for a very long time as long as you rinse it out every once in a while. The only real purpose of the filter pad is mechanical filteration. The carbon in there doesn't really last long and eventually turns from chemical filteration to biological filteration.
All you really need carbon for is
1. aid in the removal of medication
2. aid in the clearity of the water (i.e. removing tannins from driftwood)
3. aid in the clearing up of a stench
You shouldnt have to worry about any of these unless you have a sick fish that NEEDS medication, put in drift wood, or don't clean the tank in a while.