Let's start at the filter and the bypass valve/switch end. What Part # filter are you currently using..? What was the original filter Part Number listed in your Parts Manual ..?
Check the wiring close by your bypass switch. Does it also go to a temperature switch..? See below which is copied straight from a Cat Service Magazine article entitled "Troubleshooting Filter Indicator Switches"
There is generally nothing wrong with almost every switch replaced in the field. These switches are frequently replaced in error because the bypass spool was not moving freely and (sticking on dirt or debris) causing the switch contacts to OPEN and indicate a plugged filter.
The root cause can also be the temperature switch. To prevent nuisance restricted filter indications when the oil is cold, a temperature switch (mounted in the filter fluid flow) is connected in parallel with the filter indicator switch. The temperature switch contacts are CLOSED at oil temperatures below the normal operating temperature of approximately 52°C (125°F) for the transmission oil filter. As long as the temperature switch contacts remain CLOSED, the filter indicator switch can OPEN without causing the filter alert indicator on the monitoring system to FLASH. When the temperature switch contacts OPEN, the filter indicator switch takes over control of the filter alert indicator.
So check your temperature switch and it's associated wiring. That may be where your problem with your plugged filter warning lies. How many hours on the machine or on the converter if different to machine hours ..?
Once you've got that cracked we can move on to the torque converter scavenge pump.