Have you tried using a trackball? Or try looking around for a Transport controller that you can hook up via USB or Firewire.
They won't be cheap, but if this is your livelihood...
The real question, then, is: how much is the health of your wrists worth to you?
I have been using a Digidesign 003 extensively for a 45-minute film I am doing the sound design/recording, etc. for and it has been a life- and wrist-saver due to the jog/shuttle wheels that it has built-in. You could look into a Mackie Universal Control, maybe. I think they run around $1,100.
Here's a standalone type:
JLCooper MCS3-SP-USB Media Control Station
Wolf
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