I do belive i see what Thomas712 is saying. The little holes in the egg crate that are not around the over flow where it goes in to the canster filter, will just hold the "junk" that accumulates (sp) in the bottom of the tank. The "junk" has no way out. It is trapped. Now, this is just my opinon, but the "extra" vacumes or more LR will help, but it would be a "band-aid" to an problem that will raise its ugly head in the future. Look at the pic below. Now it is just something that i created in PS, but it hopefully will do the job. See all the "junk" it will allways be there in some shape or form. No matter how much live rock you have, or how may times you vacume. It has no where to go, it can not get to the drain hole (reddish-pinkish circle) that feeds your filter. Only the blue spots will be clean.
But, on a good note, you are still ok. What i would do is to go to HD or some where and get some sand. SD or what ever. I do not have access to SD in my area, so i used quick create play sand. Real cheap. Like 2 bucks for 50#'s. Take the CC and the egg crate out. Build you a wall around your holes with some Plexi Glass, once again, real cheap at the same HD store. Get you some aquairum (sp) silicone and seal it up. Let it go to the filter. Dump the sand in there until you get about 4 inches of sand. This set up will assure you of a good, low maintance tank for a long time. Then go out and get your LR, let it cycle, and then your good to go.
BTW, just because is says "shark" under a guys name, does not mean that he/she knows everything about everything. That is why we have this BB, to share, and pool our knowledge.
(No disrespect to the sharks
)