Which hand mill do you have, left or right ? That would be which side of the mill is the blade/husk located, left side or right side ? Take a straight edge and hold it against the blade, as close to centered as possible, to see which way the blade is cupped. It should lean toward the husk and stand up straight when up to speed. 690 RPM is probably close to what you want with a 48" blade. My 52" was hammered to 600 and I had to raise the throttle set a little over time, and it was at 670 when I sold the mill.
When you did this (I removed and cleaned the surface rust from the shanks and teeth), did you mix up all the shanks, and just reinstall them as you picked them up ? Reason is, sometimes 1 or more sockets will be worn, and, a sightly larger shank will be installed. Changing that
could mess up the blade geometry(wobble-waving).
1/32 to 1/16 should be good for lead. Some people will push the guide pins against the blade to adjust lead. NEVER do this. The blade may rest against the pins when not turning, but, when powered up, it should NOT run against the pins. They are for holding the blade in line when sawing through a knot or tensioned-compressed stressed logs. Blade should have 1/16 or so clearance on both sides as it is running at speed. What type wood are the pins ? You can use dogwood or black jack oak as guide pins. They will wear like iron.
The mill I had "Corley", had adjustable shaft bearing holders. Loosen the bolts that held the bearing block in the holder, and tighten one, loosen the other. IF you don't have that type, proceed with caution. You do NOT want to get the shaft out of line and heat up the bearings. How many bearings on the shaft, 2 or 3 ? IF 3, you need to move both end ones and allow the middle one to float, until you tighten both end ones up, then tighten the middle one.
Once you are ready to saw, throw a dab of lube on the blade. I used to have a 3 pound coffee can, half full of diesel fuel and a couple shots of drain oil. Had a scrub brush standing on end in it, and, every so often, just sling a bit on BOTH sides of the blade, while it is turning slowly. Too much will get thrown off and make a mess. Keeps the blade slick and helps cooling a little.
I also would sling just a little on each log bunk before loading another log. You will be amazed at how easy it is to turn logs this way. I did the same with our band mill bunks.
Don't worry about the diesel and drain oil messing up your lumber. Just a little bit goes a long way.
You might try using a straight board on the carriage and butted up against the head blocks. That way, when you advance the head blocks (board), you can see if it is advancing evenly. Then set your lead to that, being sure the blade doesn't get too close to the bunks. Should have ½"-¾" clearance.
I always used a 10" mill bastard flat file to sharpen the teeth. Slow steady STRAIGHT strokes, and only take enough to keep the tooth corners sharp. Not filed straight across will cause the blade to lead. Most guys then, start adjusting stuff. Go slow and pay attention. Lots of guys use the Jockey sharpener, some electric and some hand turned.
Does the carriage have pillow block trucks, or axle holders, or, are they bushings ? If you don't know, take a 2 X 4 and try to lever the carriage across the tracks, side to side. You want "0" movement sideways. That is where thick and thin lumber could come from.
I'm somewhat familiar with B'ham, but, not interested in football, at all. Hockey is my sport, and, FIM Speedway dirt motorcycle racing. Needless to say, I don't participate in either of those, just enjoy watching.
Photos of your mill would be nice, so we can maybe spot something. B H Payne is a good outfit. Dealt with Ric or Richard, ? maybe, the owner, when I bought new blades for my Peterson Swing Blade Mill and also a dozen gang saw blades from them.
Hope this helps. If not, let us know and we will do more guessing.
Harold