Ok - Jacob - that "dark brown" that you saw, was the detritus that was stuck/hidden IN the substrate for a long time. You have now released it into the water column. Which means that the denitrification cycle is now having a hard time breaking the detritus down to ammonia, and from ammonia to nitrites, and from nitrites to nitrates.
Added to that, the released detritus also most likely leached phosphates in to the water, giving "food" the the nuisance macro algae spores, giving them "reason to live" ;-)
Therefor the algae problems...
Here are some possible solutions that you can try:
- run a sponge filter (temporarily) to catch up as much of the detritus you can (do you have a spare canister filter - usually you should not use a canister filter, but in this case, you might need to - temporarily)
= remember to clean out the sponges every 3 days
- do HUGE water-changes - e.g. 25% every week (weekends) for the next 4 or 5 weeks
- buy some phosphate remover (ie SeaChem PhosGuard) and run this in a high flow area in your tank's sump
- make plans to replace your current substrate (which sounds like the particles are MUCH bigger than 1.5/2mm - causing the detritus to be trapped) - with some substrate that have sand particles that are smaller than 1.5mm at least - either playsand (ask at Reggie's Toy World/Toys-R-Us, or perhaps even Builder's Warehouse), OR use aragonite/carib-sea (MUCH more expensive usually)
- run your skimmer very wet for a few weeks that the crap be removed from the water column
- constantly (on a daily basis) stir up the top layer of the substrate to get the detritus into the water-column...
This whole thing will take a while to get rid of....
You should also reduce the lighting period of your lights (to a maximum of +-5 hours in the day), AND feed your fish less - try feeding only dried food ONCE a day...