Upon further inspection I found a vacuum line for the transmission that had completely come apart and disconnected itself from the module on the front of the firewall. I went to the dealer and ordered a bunch of connectors and misc vacuum lines, along with both fuel filters and new o-ring gaskets.

I'll keep you all posted if it makes a difference.

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1963 Ford F100 - Cummins Swap?
1985 Mercedes 300SD - 210K
1992 Ford Festiva - 92K
2001 Ninja 250 - 8K