I found it hard enough to manage 8 instances across two servers. i couldnt image trying to manage 36.
What i found interesting is this... Are you saying that you maintain one jvm.config across all 36 instances?
Thats actually a great idea and never thought of that. If that is indeed the case, any special permissions needed when sharing the file? Did you hgave to change the account CF runs under?
for the configuration you could align the neo-*.xml files in WEB-INF/cfusion/lib/ between your servers
for the patch and updates you could align the jar files in WEB-INF/cfusion/lib/updates/ , but some patch require to update also some other files in different location (like the one in the CFIDE ), so it's something would be better to evaluate everytime..