Well, if the required protocol and devices are truly not resident in your remote, you will still have to load (as a minimum) the protocol upgrade and a bare-bones device upgrade (no button assignments).
But then, either in KM, RM or directly in IR, you can create keymoves, using that device upgrade.
I would bet, however, that there is a resident device in the 2116 for at least the Pioneer and Yamaha units. Even if they don't automatically map all of your functions, you can use the built-in devices to make keymoves. Check
THIS spreadsheet to see what setup codes may meet your needs.
For example, it is likely that you need the Pioneer DVD (setup code 0525 or 0571). These are NOT in the 2116, BUT the setup code VCR/0568 uses the same protocol (PID: 007E) and device numbers/fixed data, so it's likely you can build keymoves calling on setup code VCR/0568, and use neither a protocol upgrade nor a device upgrade for your DVD player.
Similarly, almost all of the Yamaha upgrades I looked at use NEC1, device 122, which can be found in the 2116 as setup codes AUD/0176, 1176 and 1276. Each may have differnet function to button assignments, but each should be a good starting point for keymoves, obviating the need for those device and protocol upgrades.
You appear to be SOL on Barco, Crystal and Lutron, but as I mentioned above, if you reduce the device upgrades to have NO BUTTON assignments, and then use keymoves for all of the button assignments in one or two of them, you should regain a measurable amount of upgrade space. Hopefully the Pioneer and Yamaha upgrade space will yield you some gains.
You might do best to upload your current IR file (and post a link to it) and someone can look at it and give you a suggestion or two.