MAX_VELOCITY = 360.0
MAX_ACCELERATION = 600.0
STEPGEN_MAXACCEL = 750.0
SCALE = 1.11111111111
FERROR = 1
MIN_FERROR = .25
I have no experience with steppers. Right now all my machine are servos.
I would lower the axis_3 max-velocity, max-acceleration, and stepgen_maxaccel to 50, 100, 100 and slowly increase them to find out where the best performance is. You may need to increase the ferror and min_ferror to allow the axis to move very sloppy until you get better performance. From your description it seems to me the max_velocity is too high. You may try just lowering it first. Sorry for not knowing more. Have you tried the LinuxCNC.org - Home users list or irc channel? Both of these are tremendous resources. There is also a forum.
the scale of 1.111 seems odd to me (but I don't have an A axis).
How did you come up with it?
the max velocity is set at 360 degrees per second can your A axis turn once per second?