Apparently I had 3 issues. First, yes, 1618 fixed the issue. I went back once I found the other two issues and installed 1617, confirmed the issue, and then upgraded to 1618 and confirmed it was gone.
Issue #2, related to this thread, is that there are more threadpool items which need to be updated on larger systems. I also finally figured out the quartz item I was having issues with above. This is the list I have right now, tailor it to your system needs:
org.eclipse.smarthome.threadpool:thingHandler
org.eclipse.smarthome.threadpool:discovery
org.eclipse.smarthome.threadpool:safeCall
org.eclipse.smarthome.threadpool:ruleEngine
org.eclipse.smarthome.threadpool:org.quartz.threadPool.threadCount
org.eclipse.smarthome.webclient:minThreadsShared
org.eclipse.smarthome.webclient:maxThreadsShared
org.eclipse.smarthome.webclient:minThreadsCustom
org.eclipse.smarthome.webclient:maxThreadsCustom
org.jupnp:threadPoolSize
org.jupnp:asyncThreadPoolSize
org.apache.felix.eventadmin.impl.EventAdmin:org.apache.felix.eventadmin.ThreadPoolSize
All of it goes into services/runtime.cfg.
Issue #3 was the Neeo IO transport. There is an issue right now with the one that comes in the regular bundle which requires the two jar files to be put into the addons folder. Apparently something with the IO file was causing other services/bindings to not load properly. This was causing a whole other set of issues which made the system look slow.
Thank you all!