1. The sequential PHA mode you ask for sounds similar to what we describe in the readme.txt describing the news of MCDWIN v 2.88, MCA3 Server version 2.77 (Mar-21-2005):
- Special chromatography support:
  PHA sequential mode with realtime preset, listmode, only one sequence. Now there is no deadtime at all between cycles, the card is not stopped for switching to the next cycle. The 2D spectra 8k x number of cycles can be as large as you like. Time resolution is any number times 0.001 sec.  For short preset times or if the PC is very busy it could be more  exact to let the card stop after each preset. You can force it by setting the "sequences" parameter to 0.

2. please make a test with external triggering using the MCDWIN software.
It is described in the manual on page 4-7:
..
It is also possible to use the digital input 4 as an external trigger for starting the system (more modules: Dig inputs 4..7 start systems 1..4) (DESY control line).  If the corresponding checkbox is marked, a start command for the respective  system will not immediately start the system. After the start command, the  digital input will be permanently checked for its logical level. If the level  changes from high to low, the data for the system is cleared and it will then be started. It will stop if the level returns to high (or vice versa if Invert is marked) and can again be restarted with the next level change. A stop command for the system will finish the digital input checking. By checking  Clear before Start the spectra is cleared before the start. A stop command for the system will finish the digital input checking.

The manual can be downloaded from our website, look in www.fastcomtec.com
under support for manuals.

3. Tagging is possible too. The 512k memory can be divided into 64 parts with 8k  size, and using 6 tag bits you can specify which part will be filled. Maybe this is a good solution, as it is not necessary to stop the acquisition. Dig I/O ports 2..7 are used as address bits. You can test it with the MCDWIN software: In the settings dialog enable "Tagged spectra" and set 64 for the number of spectra,
8k for the spectra range. 8k x 64 is the only possible range due to the fixed  conversion ADC and using tag bits wired like ADC address bits. See in the manual on page 3-9 for tagging and 3-6 for the Dig I/O port.

4. A possible solution could be running the acquisition in a loop, for example with realtime preset, and controlling the mechanical stage via a small program between the acquisitions. Using our software this would be possible using  scripts. For example you could write a small text file named loop.ctl containing:

onstop run next.ctl
numruns=256
onlast run loopend.ctl
start

The file next.ctl could contain:

exec movestage.exe
start

The program "movestage.exe" should move the mechanical stage to the next
position.

5. Another possible solution could be using the Dig I/O for moving the stage. With the MCDWIN software you would in the system definition dialog enable "Value incr. at Stop"  The value output at the 8 Dig I/O lines should then control the position of your mechanical stage. You could use the scripts above, but instead of the line "exec movestage.exe" enter just a command for a suited delay, for example  
delay 500 
that means a delay of 500 msec before starting the next acquisition.