You should discuss the shims with your fitter if you used one. I'd think the shims are more about correcting knee, ankle or foot issues or keeping you from having those issues. I'm not too sure shims will affect the issue you described. But I'm not a fitter. I'm only experienced in what has worked for me. And shims aren't uncommon for anyone using road cleats. I use SPD cleats on my road bike, so I've no experience with shims for cleats or shoes either.
If it is abrasion, then some people swear by chamois creams such as Chamois Butter and even Boudreaux's Butt Paste for diaper rash. I've never used them. I haven't had a saddle sore but once or twice when I still wore underwear beneath my shorts. And I have had none in the last 12 years.