Get some CLR from the hardware store, pump as much as you can in there and let it sit. Rinse, repeat.
IF you can get them cleared enough to get some flow, even a little bit, you'll want to rig up a flushing system. Fortunately that's as easy as some hose fittings, a 5gal bucket, a cheap submersable pump, and a cheap garden hose you can cut up. Connect the sump pump to one side of the heater, connect the heater outlet to the other heater inlet, connect a hose from the second outlet and clip/tape/tie it so it dumps into the bucket. Put the pump in the bucket and grab a few gallons of either CLR (expensive but WOW does it work) or white vinegar (cheap but takes longer) and fill the bucket. Let that circulate for a few days until the outlet pipe is flowing at full volume. Then re-flush with clean water a few times and plumb it back in.