I pushed down the top piece of the seal over the transmission shaft (with the rubber o-ring facing down) I used axel grease on the spin bearing.
Oops! prepare to disassemble unit and flip the top part of the seal so that the bronze disc contacts the ceramic face of the boot seal, then work the rubber ring carefully into the centre of the disc, compressing it so it remains tight to the shaft. Do not use any lube on this seal - not a good idea to put grease into the tub bearing either as it will accumulate underneath and "gum up the works". The bushing is oilite so it has oil (not grease) injected in it during manufacture.
As for the springs, the one that doesn't match with the other 2 will have more tension and gets installed 180 degrees from the motor so it offsets the motor weight and aids in balancing - and yes, you can install the other agitator for your style of transmission. Did you use the electrical duplex boxes to extend and hold the springs open during disassembly/assembly ?
Transmission part link ==> Transmission