I did some troubleshooting. The latency disappeared when I turned on plugin safe-mode. I started at the end of my list of plugins and turned them all off, tried typing to see about the latency, and then turned them back on. The culprit in my case is the Checklist plugin. When enabled, it cases the 1 to 2 second latency when typing, and the 40 minute indexing time. I disabled the plugin, and repeated my uninstall and reinstall routine. This time indexing was maybe 5 seconds, and I have no CPU/latency issues with it disabled.