Should I take the rock back out and clean off or let it go and if I do let it go will I have to clean it at some point later before stocking?
No, you can leave the uncleaned rock in the tank - it will take a bit longer to fully cure (depending on the amount of dead sponges, algae, etc. on the rock...) but in the end everything dead will decompose just the same. As they decompose the dead organisms will be consumed by microscopic organisms and bacteria, and will disappear naturally, so no need to clean the rocks later.
If you're lucky some "dead" organisma might even recover and survive the cycle.
Does lighting and temp have any importance while cycling?
Yes and no :y220d:
A higher temperature (within reason, obviously) will cause bacteria to multiply more rapidly, and will thus speed up the cycle IF there is enough oxygen in the water. A higher temperature will, however, decrease the level of dissolved oxygen in the water, and there will be an optimum temperature for any particular system (depending on water circulation, skimming, living algae, etc.)
Should I add the powerhead now while cycling to get better circ?
YES! The better the water flow (and surface agitation), the more O2 will be available in the water. With higher flow the availability of O2, food, and waste removal to/from the organisms/bacteria in the rock and/or deep sand bed will also be better, thus allowing for a higher concentration of bacteria/organisms per area of substrate.
Will there be an issue when I swap the filter for the skimmer when the cycling is done?
If you are planning to use live rock and/or a deep live sand bed as your "filtration media" you should not run any filter media in the Aquaclear - just use it to increase the water circulation.
If your LR has much dead growth on it, I would suggest that you start using the skimmer from the start of the cycling process. Although doing so might increase the cycling period by a few days, it will help to moderate the ammonium spike, and might thus save some organisms from being killed by the ammonium/ammonia - and after all, you paid good money for the "life" in the live rock...
And how long should I expect for the cycling to complete?
How long is a piece of string...
The ammonium spike should peak after about 2-3 weeks, with the nitrite spike peaking some 10 to 14 days later.
In my opinion a "cycle" is only complete when the nitrate level has peaked and returned to zero, and this could take another month or two.
Hope this helps
Hennie