Hi Devin...maybe a 'clean' TTPUB configuration will help.
Here's what I did to get the current MTS gtfs data running in ttpub:
1. Downloaded and unzipped the .war.zip file, installed the .war
file and started tomcat.
2. Let tomcat unwind the .war file, then shutdown tomcat.
3. cd tomcat/webapps/ttpub/WEB-INF/classes/org/gtfs/
4. rm -rf configure
5. mv blank-config configure
6. rm -rf schedule
7. mv .../mts/gtfs schedule
(NOTE: could do the same thing in a different way by editing tomcat/
webapps/ttpub/WEB-INF/classes/TimeTablePublisher.properties, as noted
the docs)
8. startup.sh tomcat
9. edited ActiveServiceKeys config and added WD,FR,TH,MF to the
existing Weekdays config
10. looked at a handful of routes, and stops & times seem good (or at
least logical) in both directions