Okay, so i've redone the airflow - the top fan is an intake now and the H50 is an exhaust. The cooler is seated properly, the first time it was reseated with fresh MX-3 applied temps were hitting mid eighties - so I removed that and reapplied some AS5. It's pretty fresh so hasn't had a chance to cure yet, but temps across the cores are much more even - 79/77/77/75 and ambient is a bit higher now. BIOS is reading 1400 RPM on the pump. Time to start fiddling with voltages.
Ambient temps are 27.2C at the front intake, and 30C near the CPU and 34C near the 4890.