Sounds like you're having fun. Okay, regarding the issues ...
1) latency. At first I was going to adress this one, but since you say you're new to linux maybe just first do numero duo. Ofcourse a latency of 400 us is going to seriously limit your stepper speed, so has to be fixed if any actual work is to be done. But 400 us latency is not going to be a problem while doing some slooooow speed jogging of the axis.
2) The pinout ... I hope you do have the pinout of the FET3 kit? If you know that one, it is a simple matter of configuring the right pinout in the right config file.
On the emc side you can configure the parport pinout in a file like for example EMC_DIR/configs/stepper/standard_pinout.hal
The default is something like
Which is fairly self-explanatory really. Check in your BIOS if LPT1 is assigned to port 0x378, and adjust accordingly. (probably correct since you do get a lot of noise from the steppers, i.e it is doing something). By the sound of it you may have to edit the Xstep, Xdir etc pinouts according to what your FET3 documentation says.
# standard pinout config file for 3-axis steppers
# using a parport for I/O
# first load the parport driver
loadrt hal_parport cfg="0x0378"
# next connect the parport functions to threads
# read inputs first
addf parport.0.read base-thread 1
# write outputs last
addf parport.0.write base-thread -1
# finally connect physical pins to the signals
net Xstep => parport.0.pin-03-out
net Xdir => parport.0.pin-02-out
net Ystep => parport.0.pin-05-out
net Ydir => parport.0.pin-04-out
net Zstep => parport.0.pin-07-out
net Zdir => parport.0.pin-06-out
After you have configured that, you should be able to do some sloooooow speed jogging to see if the connections are right. After that it's time to do something about that latency.
Hope that helps,