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Super Moderator
1966 Crown Coupe, 2016 200 S AWD, 1962 Lark Daytona V8.
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23,870 Posts
The whine may have been from the front pump and not the torque converter. If the ATF coming out of the cooler hose has air bubbles in it, there may be a suction-side filter/pump sealing problem. There may also be an internal leakage issue that is keeping pump output pressure low.
The filter o-ring is important and can fall out of place. I have found filters with the old and the new o-rings together in the pump intake hole that didn't allow the filter to seal. The old ring usually stays in the hole and doesn't come off with the filter. It can be overlooked. I have also found valve body bolts loose. Any pump suction-side leaks will cause poor pump output.
The cooler output fitting is the one closest to the engine, correct?
A regular engine code reader will show the PCM generic P0700 transaxle fault code. You need to scan the separate TCM for fault codes which a basic code reader usually can't do. The TCM fault code(s) may help here. Don't guess at parts.

Diagnostics here: http://www.scribd.com/doc/47304900/81/P0944-LOSS-OF-PRIME

TSB here (although it doesn't cover '01's, the same thing may be happening): http://www.ertyu.org/steven_nikkel/neontsbs/2003/21-004-05.pdf
 
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