Are you cooling just the CPU?
Did you dismount/remount your wbs in this change? Which wb(s) are you using?
You mention the mcubed flow meter and water temp probes - but don't provide any data from it. Why rely on mboard-provided temps? Comparing the before and after flow numbers might tell you if you now have a restriction.
All that said/asked - you might find it interesting to replace your silenx fans with ones that push lots more air - just to see what happens to your temps. You should be able to do this without disturbing the rest of your system. Not seeing much change in temps would indicate that your "weakest link" is somewhere else - or that there's something wrong with your temp measurement methodology.
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