I am sorry to hear that he did not make it. Alot of times it is hard to go through that, but I always like to point out that at least some good can come of this and you can now be a better fishkeeper for your future aquatic friends!
I think that your plan to get things right before adding new fish is great and really what you need to do. I would do a bit of 'round robbin house cleaning' here and start to take out small portions of your substrate and clean it well in either a colander (spaghetti strainer) or with another method you can figure out. This will greatly reduce the amount of waste in your tank and slow down the bacterial/algea blooms.
Realizing that you still have your pleco in the tank (right?), just keep in mind as you are putting the substrate back in the tank that your pleco is going to be making A LOT of wastes, most often in very long 'strings' that you will want to be able to remove from the tank as easy and efficiently as possible. For this reason, i would take a good look at the size of your substrate (i.e. Is it sand? Small gravel? Large gravel? Pebbles? etc...) and decide what the largest amount of substrate in your tank can be without risking a lot of wastes getting trapped inside it and underneath it, where you are going to have a hard time vaccuming it out. This will help you immensly in the future.
The basic idea here, and a lesson I learned very recently, is that a tank should obviously be a good environment for the fish, as well as be great to look at and watch, but also very 'user friendly' for yourself and your lifestyle. Even though at this time in my life, with working full time, going to college full time, having a wife and kids and my passion for this hobby, I have about 1/2 a second of time to spend cleaning tanks, I have been able to stay far ahead of most problems because I have them set up so I can take out the water while vaccuming the substrate, and then refilling and walking away. Try to keep this in mind as well because even if you arent very busy, you are going to want to ensure that you have the highest probrability of success which usually falls under my life's plan, which is KISS...keep it simple and stupid!
FINAL UPDATE: Cichild/tank problems. 
