A plugging ATF filter can cause a whine like a power steering pump. The pitch will will rise and fall according to engine RPM.
I would first drop the pan and look in the bottom for sediment and debris. Clean the chip magnet, Replace the filter and use ATF+4 only. Make sure that it says that it meets Chrysler MS-9602 on the bottle label (like Walmart SuperTech ATF+4). A refill will take about 4-5 quarts.
Some filter kits come with a new pan gasket. The factory uses ATF-resistant RTV. Rubber gaskets are OK, cork gaskets are obsolete.
The front pump whine is probably because the pump is suction-loaded, not necessarily from a 'bad' pump.