Getting started with 6i25+7i75+7i85s

Dear gods, I've got the cards mentioned in the subject, and my purpose is to run a lathe with:
- STEP/DIR steppers for x and z axes
- quadrature linear encoders for x and z axes
- Argon servo drive to run the dc spindle motor
- a stepper, a solenoid and an absolute encoder for a tool carousel (although this one might be easier to control with a separate microcontroller?)
- relays for coolant and lubrication pumps

I've found that PncConf does not have the firmware option for my selection of cards, and now I have little clue as to how to proceed.
Why I'm in such a pickle is that I had a friend pick those boards for me, but later, he has become too busy to help me with setting them up.

So, I suppose my question is what should I do? Money or sunken costs are really not an issue. If I should buy new cards that are easier to setup, or pay someone to guide me, then I will.
Oh, and I do also have a 7i73, but no panel or pendant built or even planned yet, so I'm not so worried about that one. For now, I will be a happy man if I can just get the machine to run at all.

I would probably start with a pncconf configuration file set
made for a 5I25 + G540. I would set the number of stepgens and
encoders to 2. Then select "accept component changes" and assign
your stepgens and encoders to the desired axis. Finally hand edit the
resulting hal/ini files to deal with the card differences. (mainly GPIO settings
for limit switches etc)

Edit: You may need to add an additional PWMgen or stepgen for controlling the spindle
and additional encoder for the spindle.

Alright, I got the card flashed with the 5i25_7i85s_7i78 firmware. (I think, info on the card printed by Mesaflash is in the text file attached.)
Now, can I add the firmware to PncConf so I can use the nice dropdown menus for at least most of the configuration or will I have to go straight to the hal/ini files?
And then, how do I figure out how the pin numbers on the 6i25 correspond to the pins on the daugher cards? I guess the general I/O taken care by the 7i75 breakout board will be easy, but what about the 7i85s?
Say, I have the step pin of the x axis driver connected to pin 12 on the 7i85s TB2 connector, and its function is /TX0. So I check TX0 from the connector pinout in the 7i85s manual, and find out it corresponds to pin5, IO8 on FPGA PRIM I/O and IO25 on FPGA SEC I/O, so is my I/O number for X Axis stepgen 8, since I have the boards connected via the primary DB25 connector?

You can use pncconfs discover option to more closely match the firmware.
(then disable the unused P2 (7I75) functions by setting the number of
encoders to 4, stepgens to 4, and pwmgens to 0)

To get the correspondence from say P3 stepgen 0 to 7I85S TB pin
you can run mesaflash with the --dbname option:

sudo mesaflash --device 5i25 --dbname1 7i85s --readhmid

Thank you. That's a lot more handy than consulting the manual for each pin.
Now, when I try the Board Discovery option, I get the following error:

PNCconf encountered an error. The following information may be useful in troubleshooting:

LinuxCNC Version: 2.8

Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pncconf/pages.py", line 914, in on_mesa0_discovery_clicked
self.a.discovery_selection_update(info,0)
File "/usr/bin/pncconf", line 1547, in discovery_selection_update
firmdata = self.parse_xml( driver,boardname,firmname,path,boardnum)
NameError: global name 'boardnum' is not defined

You may need to update to 2.9 for the pncconf discovery option
to work, or just use the g540 option to start

Updated to 2.9.3, looking better, even got the axes to move. Though, now when I try to modify the previously created configuration, I get the following error and can't proceed.

LinuxCNC Version: Master (2.9)
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pncconf/pages.py", line 107, in
on_button_fwd_clicked
if not self(): # prepare returning True skips that page^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pncconf/pages.py", line 1012, in mesa0_prepare
self.a.init_mesa_options(0)
File "/usr/bin/pncconf", line 2157, in init_mesa_options model.append((cur_firm,))
File "/usr/lib/python3/dist-packages/gi/overrides/Gtk.py", line 1016, in append
return self._do_insert(-1, row)
File "/usr/lib/python3/dist-packages/gi/overrides/Gtk.py", line 1007, in _do_insert
row, columns = self._convert_row(row)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/gi/overrides/Gtk.py", line 899, in _convert_row
raise ValueError('row sequence has the incorrect number of elements') ValueError: row sequence has the incorrect number of elements

At some point you may need to move on from the GUI and make changes directly in the hal/ini files

Thank you very much so far, gentlemen.
I've gotten the lathe to run, but now, when I try threading with it, I have two curiosities.
First, The lathe can accurately thread only up to about 150 mm/min of z feed. Faster than that and it no longer stays synchronised. This is not a big deal, but seems odd as my z axis moves up to 1200 mm/min.
Second, more significantly, when a threading program is rerun, it is not synchronised with the previously turned thread, but picks a new, seemingly random start. This happens only when a program is rerun. If a single program has multiple passes, it keeps them lined and the thread turns out fine.
For spindle speed, I have timing belt driven quadrature encoder that puts out 3000 pulses per spindle revolution and a photogate reading a plate with a single slit mounted directly on the spindle for the index pulse.
Any leads on how I could go fixing these?