The hydraulic system does have enough play to account for the difference in thickness but you will need to account for it with the length of your pushrod. A mechanical linkage from a CJ has a screw in adjustment to the length of the pushrod, so you could adapt one of those as a means of adjusting it, or you could experiment and find what works. I personally am not willing to deal with making it work, and there is a possibillity that it won't work.
I had a nightmare with my Spirit when I switched from 9" clutch to 10" clutch. It should work but it doesn't. The mechanical linkage didn't have quite enough adjustment. I'll never put my self through that again.
I do have an AX15 internal slave, NSG370 6 speed, and NV3550 external slave ready to install in an Eagle in my garage. My CJ8 Scrambler also has the Advanced Adaptors kit with T5 bellhousing, flywheel, clutch, and linkages with a NV3550 behind it. Any specific questions about them?
There are two types of 4.0 flywheels. The NSG370 CPS notches are clocked differently than the AX15 version, but its otherwise identical.