You should be looking at editing the
ai_profiles.tbl. Depending on the depth of your mod, you may want to make a new profile, and have your missions use that, or you may want to write a tbm and just modify the existing FS2_RETAIL profile. Either way, you probably want to edit:
$AI Always Links Energy Weapons:
FS2 Open, 3.6.10 or earlier:
* AI ships will link energy primaries if energy levels are greater than these percents.
* Syntax: Float list
o Default: 100, 80, 60, 40, 20
$AI Maybe Links Energy Weapons:
FS2 Open, 3.6.10 or earlier:
* Defines the same as $AI Always Links Energy Weapons: but in situations when its hull is below 33 % of maximum hitpoints.
* Syntax: Float list
o Default: 90, 60, 40, 20, 10
Granted, it sounds like your ships should have already been linking up at least some of the time since they should be at full weapon energy, do you have the game on a higher difficulty as well? Otherwise they will likely not link up weapons very often.