Diva,
Dont feel bad about Bubbles, honestly fish are hard to keep, its not as easy as people think ( I didnt know a bowl was cruel when I first looked into keeping fish..) You are doing loads of things right, and the main thing is, you care enuf to want to do even better. Many fish owners could learn a thing or two from you, so dont feel bad!

I am a bit worried about you pH in the tank. If you have the money go invest in a kH (and gH) test kit, and while you are out buy some baking soda. If it continues to drop we will need both! If you can find your kH readings for the tank this determines the "fixedness" of the pH of your water, (it acts as a buffer to pH swings) you are looking for a reading of 120 - 150 ppm, do a test on the tap water and the tank water for everything..btw ( just once on the tap water, my tap water has traces of ammonia in it, so I know when I water change to expect to see this etc..) If the pH starts to drop more rapidly over the next few days ( a pH crash) I would post on the boards asking for some advice... but generally a teaspoon of baking powder (raises the buffer capaxity)for every 50 litres of water, will be the ratio to higher the pH. You do it and test before adding more. Fish can tolerate a gentle change in pH but not vast changes so if it now settles at 6.8 thats ok, its if it keeps dropping you need to worry. You dont want to keep having to mess with the pH tho, hence asking the forum for some better advice on long term solutions. ( I am not knowledgable on the subject!) You can use baking soda in a weekly maintenance schedule but you'd need some more details on this. So yep, keep a check on the pH closely for a while, and with most other things, water changes will help in the short term.
Having a bit of a think here, seeing as it was 7.5 out the tap... if it was my tank, i'd probably add just a teaspoon of baking powder now, it does seem that you have a low kH value and this will help keep the pH level more constant. Rapid pH drops towards acidity cause "acidosis" which can kill fish...add a teaspoon, and have a retest of the pH... remember you want the rise to be gentle! You might also want to look out for some oyster shell grit, keeping some of that in your filter can act as a better long term solution to pH issues... I still havent spotted it in the LFS yet, but if you are there already? If you start to worry about the pH now, pop up a new post to get some helpful hints, or do a "search" on the boards, and there are plenty of replies to posts with tonnes of helpful advice!
Just to check, you arnt using amquel are you? ( it effects kH alot.)
okies, nitrate next!

IMHO ideal nitrate levels should be less than 20 ppm. Tho up to 40 is acceptable I think, regular water changes will keep the level low, hence water changes even in a cycled mature tank especially if you dont have any live plants ( which take up the nitrate). So back to checking your tap water here, if its got nitrate in it of 10 ppm it'd be daft to try and get your tank lower than that amount! Once again we are back to water changes keeping things healthy!
Gravel... well...I think that depends on person to person.. lots of people at Koko's have barebottom tanks... they find it cleaner and easier to keep clean. Unless you have an undergravel filter, I would say about an inch of gravel is enough, my syphon seems to let me clean that quite well, and runs clear with regular changes... you have lots of fish, thus lots of poop, so you want to make things easy to keep clean. Remember as you disturb the gravel you can release toxins, so maybe work on a small area per clean?
If you havent introduced anything new to your tank recently its more likely to be your water chemistry causing issues, rather than diseases. Fish do yawn like we do, but if you suddenly catch them doing it ALOT, post here, and we can have a review of the issue

Bubbles might not have been quite as hardy as his companions so was more suseptible to a small change in water conditions, it happens to even experienced fish keepers who are guru like in their knowledge. You have a huge resource base at your finger tips now, shout up with any questions, ask for help, and hopefully we can keep the other ones healthy

oo and take a photo soon, cos I'd like to see them