Yes, you can align yourself.
Yes, there is s/w that indicates alignment.
No, most disk alignment s/w can not be copied or downloaded;
For the better programs that I use, the disk is the alignment
reference tool. It must have the tracks in precisely the right places.
However; I find that if games, etc. are protected, they may not load
because of a speed inaccuracy. Speed is much easier to adjust.

You can go mad trying to set head alignment by loading a commercial
program, but you may want to try.
Head alignment is shifted by loosening the two screws on the bottom that
hold the mounting ears of the step motor. Then the motor is turned a tiny 
distance and tightened down. Turning all the way end-to-end of the motor mounting
slots covers 2 - 3 tracks, you want to move by quarters of a track, at most.
You need to know more before you mess with the head stop adjustment, pray it is ok.

Speed adjustment is done by making tiny tweeks of the speed control pot, 
a subminiature square plastic trimmer pot. It is in different places, top and
bottom depending on the model/year of the drive. It is on the actual DRIVE 
frame, on a rather small pc board, not in the large 1541 chassis or main board.
The drive flywheel under the floppy hub MAY have a radial pattern of black lines
that can be strobed under neon or fluorescent light to set the speed.
S/w can also measure speed, it all depends on what you can get.
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Speaking only for myself:  Bill Mays
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/  \  my mark.