It's possible that one phase of the 3-phase stator isn't reaching the regulator due to a connector problem or a dead diode in the regulator's rectifier. Either one would reduce the system to single-phase operation and greatly reduce its output capability.
A damaged rectifier diode is difficult to test in a fully potted regulator, but you can check for a shorted diode. With your multimeter in diode check mode, test each of the pin pairs (1-2, 1-3, 2-3) of the regulator connector in both directions. You should get no meter response (open circuit on all tests). If your meter does detect a diode (voltage drop of around 0.7V), then there's a shorted diode in the rectifier.
Unfortunately, success on that test doesn't necessarily mean that the rectifier is undamaged. If a diode is blown open, it will test the same as a good rectifier. You would have to substitute a known-good regulator to determine if yours is faulty.
Check the stator-to-regulator harness connectors for contacts that aren't seated all the way into their connector housings. Make sure the connector plug is fully seated into its receptacle. Look for connectors that show heat damage.
If you find a heat-damaged connector, and its housing is rectangular and made of grey plastic, then it's possible that your engine did not have SI-912i-024 performed. This SI calls for replacing the factory-installed stator harness connectors (Deutsch DT parts; rated for 13A per contact) with a more robust alternative (Amphenol ecomate RM: round, metal, twist-lock, 45A per contact). The replacement connectors are available as a kit from Rotax parts dealers (part number 481510, $458). They require specific and expensive tooling to crimp their contacts (see here and here -OR- here and here). The connector parts are available from Mouser for $71 (here).
If your aircraft is Experimental and you're able to use an alternative method to comply with the SI, then consider using Amphenol ATP connectors instead. They're very low cost and are rated for 25A per contact, which is more than adequate for this application. See this parts list for everything you'll need. Buy a couple of extra pins to practice crimping with.
The genuine Amphenol crimper for this connector's contacts is the last item in the parts list. If you want to save $12, there's a good quality crimper available on Amazon (Iwiss / iCrimp IWD-12).