You should be able to download the upgrades directly from the HK-50 and 51 consoles. If you do not see the option, use KSE (Kotor Save Editor) to manually give HK-47 2 points in Dexterity and a +3 attack bonus.
If the only problem is the HK-51 console, go up a level and reactivate the HK-51 line from the console in the munitions room. That should give you control of the production console. If you haven't already, also be sure to grab the core upload console from the floating maintenance droid.