I hope you remembered that once you get them set up in Windows you have to go to Aces High setup choose joystick area and assign the correct axis to the correct stick or pedal device. This is often overlooked and can cause that problem.
I have all USB stuff now, but had the same setup you have before. It took a bit of time to get Windows to see the analog pedals without an analog stick, but it can be done.
In Windows I chose a new stick, and you have to search around for what might work, made sure I had rudder pedals checked, and then clicked passed the calibration for the stick to get at the rudder calibration. This worked fine, but an easier method is to take that old analog stick and plug it in the gameport along with the rudders. Check rudder pedals when choosing a stick and calibrate both stick and pedals. Just leave the old stick on the floor out of the way.
Again, make sure you go into AH joystick setup and assign the axis to each input device. If you have toe brakes on the pedals assign them also.
Make sure you have Direct X 7a
Ranger Bob