Mark, you are just going through growing pains. You have to be patient and find the best method for you. I have tried them all and I have to say I successfully failed at the many sheets shuffle tray method. I tried it twice and like you I got gouges on the sheets from the corners, uneven development, etc, etc. IMO trying to do too many sheets in one time is a waste of time and money. Just think, if you had done one at the time, you would have gotten all of them fine. It does not pay to be impatient in the darkroom.
TMY in pyrocat will give you all the expansion and contraction you will ever need.
For the Unicolor tube, you need to put a lot of solution in it, if you put too little you get aerial oxidation of the developer and streaks. I have not seen your negatives but I bet if you double the amount of developer you are using you will solve your problem. Pyrocat is cheap, dont be stingy with it.....If you can, go to home depot and get the tubes they use for storing welding rods. They are awesome! Mike Pry sent to me some and they are absolutely perfect for this. If they are any color other than black, you might have to paint them, but I assure you, it is worth the time and trouble.