hi andy,
according to the A5 and 30 code you have software revision A5 and the function code is 30 which indicates that by default -non-slab option, -motion alarm, -lift/drive cutout is enabled.
i figured you might find some wiring issues, hopefully you replaced the harness?
repairing it may or may not work if there is any damage elsewhere in the harness.
that quick flash of the 01 is probably normal on startup, it may do that until it sees the ecm configuration and passes it. as long as the code goes out the ecm should be functional.
as for the alarm sounding on every function? that is what it's supposed to do, it's part of the motion alarm function while operating the unit.
If you're still not getting any motor operation but the indicators are sounding when you activate a function you should go to the motor circuit and check to see if it is being commanded to turn on. also check the motor brushes etc and make sure there is no problems with those, wear, excessive carbon buildup, etc.
if you've been messing with the relays and have moved any connections make sure you put them back the way they were. get the service book from genie's website and make sure it is number 84700 version. There are diagrams in it that will show you the wiring connections for each relay and everything else.