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If you need startup jogging and you need to tune the servo ... you need to turn off Lag monitor under the  Axis X.. Parameter ... Monitoring: Position Lag Monitor = False ...

If you have reduction factor ... you will determine it in the nominator and denominator rows somewhere in the drive manager ...

Yes one motor revolution == one encoder revolution ..

Yes HD should reverse you motion .. every odd 

This setting you generally free enable movement... next tune or you will need firmware update to start autotunnig the servo system ..

How did you wire your home and limit switches?
If you push the siwtches by hand, do you see the "pins" change in halshow?

I would recommend to wire the limit and home switches to the servo drives DI inputs.
Then you can see the signals in PDO 60FD.

e.g. add this to your ethercat-conf.xml for each A6 servo:

<pdoEntry idx="60FD" subIdx="00" bitLen="32" halType="complex">
<complexEntry bitLen="1" halPin="limit-neg" halType="bit"/>
<complexEntry bitLen="1" halPin="limit-pos" halType="bit"/>
<complexEntry bitLen="1" halPin="home-switch" halType="bit"/>
<complexEntry bitLen="13" />
<complexEntry bitLen="1" halPin="din1" halType="bit"/>
<complexEntry bitLen="1" halPin="din2" halType="bit"/>
<complexEntry bitLen="1" halPin="din3" halType="bit"/>
<complexEntry bitLen="1" halPin="din4" halType="bit"/>
<complexEntry bitLen="1" halPin="din5" halType="bit"/>
<complexEntry bitLen="1" halPin="din6" halType="bit"/>
<complexEntry bitLen="1" halPin="din7" halType="bit"/>
<complexEntry bitLen="1" halPin="din8" halType="bit"/>
<complexEntry bitLen="1" halPin="din9" halType="bit"/>
<complexEntry bitLen="7" />
</pdoEntry>


I use negative logic. You have to configure this on your drive to match the limit/home switches. This is permanently saved in the drive.
e.g.
# set operating mode
ethercat upload -p 2 --type int8 0x6060 0x00
ethercat download -p 2 --type int8 0x6060 0x00 8

# set "active low" DI input logic
ethercat upload -p 2 --type uint16 0x2004 0x02
ethercat download -p 2 --type uint16 0x2004 0x02 1

ethercat upload -p 2 --type uint16 0x2004 0x06
ethercat download -p 2 --type uint16 0x2004 0x06 1

ethercat upload -p 2 --type uint16 0x2004 0x0A
ethercat download -p 2 --type uint16 0x2004 0x0A 1

You also have to set homing mode  (PDO 0x6098) - see manual