I took a look at a sample tuning file from a '15 2500 with the 6.4. Available options for "trans type" are: 40TE/41TE/41TEA, 42RLE, 545RFE/65RFE, 62TE and 66RFE. This is not looking good - I don't see a manual option here. I assume they stopped using the "manual transmission" vs "8-speed transmission" to differentiate between models and switched to the more specific "trans type".
I have not yet bought the tuning tools and software so can't test this out. Maybe OP can confirm if the '17 6.4 uses the same format, and if toggling "manual transmission" here can fix engine error codes when the 66RFE sensors are gone?
Under Engine > Fuel > Lean / Fuel-Saving there is the option to disable MDS so that should not be an issue. Everything else seems doable with AlfaOBD. The "trans type" issue looks like the last missing piece to me.
PS. Among all the different GPEC2A operating systems, only the Ram with 6.4L seems to use "trans type" rather than the toggles below it.
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