To the OP, it seems to me your shoe-shim solution made your two legs functionally more equal, hence you should have been able to fine-tune your saddle height, tilt, and setback as does one with normal legs. Forgive me if my thinking here is too mechanistic, and for neglecting the effect of your arm challenges. In my experience regardless how carefully I set me saddle, if it is too low I feel excess pressure where my feet meet the pedals. There is a sense I’m driving my feet through the pedal at bottom trying to extend my legs even though there is not enough room. The stress also shows up as knee pain and I haven't noticed any effects in my hip joints.

What I do then is raise the saddle a millimeter at a time, revisit tilt (because tilting nose-up lowers the saddle at the rear and I’m back in the soup!), as well as setback. A micro-adjusting post is essential. After a few iterations I’m back to hood balance, pedal reach and saddle support.

So, can you use your previous set of adapted shoes and compatible pedals on the new bike? If you lower the saddle to adjust to your shorter leg, I worry that your longer leg may become constrained and stressed.

Considering that you have a set of physical issues, probably the best thing is to go back for another fitting. But does the gravel bike really need to have different contact points than the road bike, below a professional level of performance?