Your timing is WAY off. That's what caused it to get hot and have low vacuum, and is probably the cause of the miss. At partial no-load throttle, that engine wants timing. It needs to be up around 38*-39* total with the advance disconnected. Initial will fall wherever it falls, but if it's too far advanced and is hard to start, you'll have to get into the distributor or send it to someone who can set it up properly. Typically, with an untouched distributor, it'll be anywhere from 12*-16*, depending on how it's currently set up. 14*-16* initial is usually a happy place to be. Remember to set your timing with the advance disconnected, then hook up the advance. It'll run MUCH smoother and cooler.
Anything you do at this point will be useless until you get that timing up. Is there something wrong with your advance canister? Severely retarded timing is VERY hard on an engine, heatwise, so get that taken care of first.
As for taking the valve cover off, it probably isn't even an issue since your timing is the problem, but I've found a very long 1/4" extension with a swivel and socket taped on the end (so it won't pull off and drop down into the 5th dimension), works very well. I can get to all of mine this way except for the bottom rear corner on the drivers side, under the master cylinder. And that's on a Mustang, which is tight no matter what covers you have.
Edit: The finger tight plugs obviously aren't a good idea, but probably not the cause of any of your problems. Of course they should be tighter though. And your port mismatch isn't really an issue either. Lot's of dyno tests have shown that on a typical mild street engine, it won't make a big difference. If you ground the heads to match, you'll either grind through or make a huge divot in the port, which would be counter-productive. I wouldn't worry about that. Also, the water is PROBABLY normal condensation in the exhaust. I wouldn't worry about that either unless you notice your water level lowering. If it was going through the cylinders, your plugs would show signs of it and I don't really see that in the pics.