The good news is the Aquaero doesn't need Aquasuite to work. So if you already saved your settings you are OK.
After uninstalling Aquasuite search the C drive for "leftovers", I think probably in Program Data folder, and go ahead and delete then try to reinstall Aquasuite.
If that doesn't work then you will probably have to reset the Aquaero.
Here is how to reset the Aquaero as written up I think by forum member Namron:

Turn off the PC and remove all connected devices, fans, temp sensors e.t.c leaving only the MOLEX 12 v Connected
Place four jumpers on the Temperature sensor connectors 5 to 8
Power on the system and wait for two or three seconds (you should hear a loud long BEEP)
Turn the system off and remove the jumpers from the temp sensor connectors 5 to 8
Connect the USB to your PC and re-start the PC, Then using the Latest Aquasuite Software Re-Flash the updated firmware to the Aquaero 5
Turn the PC off, Connect all your sensors again and re-start the PC

Did you try a simple reboot? I had AS12-2 crash on me once at startup. I shut down the system and restarted, it never happened again.

I attributed it to a random electron fart.

So did you try resetting the device? I can't say for sure it will solve your problem, but if nothing else works that's pretty much what you're left with.

Before that, though, you might try reinstalling Net 4 full version, maybe it became corrupted somehow.