*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Oggie,
I am dealing with a similar issue right now.

Yes, if you change the laser wavelength, you will have to change settings
for a particular AOTF channel in the driver that controls the AOTF. This
would be the frequency and power (amplitude) of the signal that is generated
by the driver and sent to the AOTF to diffract a particular laser wavelength.
This cannot be done from the FV1000 software.

  If you open the laser combiner box on your FV1000, you will see that the
AOTF is from AA Optoelectronics  (France), as is the 8-channel driver. The
driver in our old system is mounted in the hinged box that sits above the
laser combiner compartment.
Your driver is probably the MOD.nc model. It has a connection for a
dedicated remote controller device. The connector looks much like for an
ethernet cable. Because you cannot get to the driver without further
disassembly, there is a short piece of cable and a more accessible connector
for the remote controller is installed on the underside of the hinged
compartment, right next to a row of six (?) switches.  So when you raise the
hinged part, you will see it.
It is true that the MOD.nc box has a serial  (RS232) connector, but the
serial interface was optional. In our microscope the serial interface is not
present, so the only way to change the driver settings is via the remote. 
The cost is in the $700 range.
Perhaps somebody at your university who plays with lasers and
optoelectronics happens to have the remote controller and will let you use
it for a day.  You would still need to know how to set the right frequency
and amplitude for your new laser.

Quanta Tech is the US distributor for AA Optoelectronic. I just talked to
them last week, they were very helpful.  If you give them a serial number of
your driver, they will be able to tell you if the serial interface is
present or not. They can also send you the instruction manual for the
driver, it includes the serial interface commands.

Assuming your laser combiner is the same as ours, you will need to take the
lid off the hinged compartment  to see the driver. The serial number is on
the front side of the red driver box, i.e. the side opposite from the
connectors. To read the serial number you will need to remove the front
panel of the hinged compartment, it is held by three screws from the bottom
plate of the compartment. 

If you are lucky and find out that your driver has the serial interface, you
can (with some difficulty) sneak a serial cable in and connect it to the
driver. A standard serial cable (NOT null-modem cable) with DB9 female
connector is what you want.

The MOD.nc driver is no longer in production. The new  MDS.nC  driver has a
USB connection, and I was told it is pin-compatible with the old driver. So
if our driver ever dies (or another of the 8 channels develops a problem), I
should be able to swap the old driver for the new one and program it via
USB.  It probably is not that simple, but I am an optimist.

Stan