Hi and welcome
Issue one should become far less of a problem as your bio-filter bio slime build up! It first clearing always takes forever but once you have active bio-slime working, the small particles tend to stick to it as they pass through the grow beds. So once things are all cycled and you have a good strong population of bacteria through your grow beds, when you stir up the gravel or add another grow bed in the future, the cloudiness will clear on it's own much more quickly. I found this to be the case with my media though mine would turn the water cloudy white no matter how much I wash before putting it in.
Issue number two. Test strips or papers are often not very accurate. Use drops or if you have a meter, calibrate it carefully and check it regularly against stuff you know have an extreme pH. I had a meter once that finally took to reading 7 no matter what I dipped it in. Problem was I didn't realize it for a while and had been trying to get my pH down in a hydro system for the cucumbers, well it wound up way down! OOps.
Anyway, well water can be interesting. When if first comes out of the tap, there is likely CO2 in it and very little O2 and if you read the pH right out of the tap, it will probably be lower than if you let the water sit or bubble it for a while. My tap water will test at about 7 right away but will be up at 8 after outgasing the CO2. I don't adjust my tap water before adding it to the system. I found that once the system cycled, the pH suddenly dropped and I needed to add shells to keep the pH up. Only bummer is the shells keep the pH at 7.6 which is a little high for some plants to get their iron. Anyway, once your system cycles, having the buffering capacity in your water may turn out to be a good thing. Only issue is you don't want to add lots of top up water at the high pH if you have much ammonia showing in the system and you don't want to add lots of top up water at any one time if the system is used to the lower pH. Changing pH should be done slowly so as not to shock anything.
#3 Bummer about the losses, at least you hadn't had a chance to name them yet and get attached

It seems a pretty common lack of patients to load up on too many fish before a system is ready for it. I fishless cycled so didn't have the worry about killing for through cycling. I highly recommend fishless cycling. That way you can even get lots of plants going long before you get fish. You just have to keep adding the fish safe ammonia source (at appropriate amounts, doesn't take much) to keep the bacteria alive and feed the plants until a day or so before you add the fish. I have channel catfish. 45 of em, they seem to be pretty tough critters. If you have any feed stores around or perhaps a tractor supply, you should be able to get some pond diet or catfish food. At least all feed stores around here carry such things. Otherwise I've heard small amounts of dog food might be ok for them till your order comes in. Or perhaps you can find a small container of koi food to tide you over till the catfish food gets there. I've used a little battery powered had vac (uses the same battery as my cordless drill) to suck up bugs and then dump them in for the fish, they really liked the box elder bugs. How many fish do you have? If you go for your worms, I would only give about one worm per fish at a time. A worm is a big mouth full for a small catfish and it can be really funny to watch. If you have plenty of aeration in your water, if a worm escapes being eaten, it will probably survive in the system for quite some time. I've added worms to my grow beds along with some worm castings for trace and micro nutrients to the plants.
Sounds like you have learned some important lessons! Now we want pictures!!!!!