Best hardware I can think of is "airframe" bolts.
For any given length, they will have a long shank and only enough threads for the nut and a few "spacer" washers.
They are ordered by "grip length" (combined thickness of the parts to be bolted together) and are available in 1/16" to 1/8" increments depending on diameter.
Naturally, you would want to use a "jetnut" (all steel alloy locknut) to secure.
I guarantee your problems will be over.
Excellent for driveshaft flanges too.