Thank you very much for sharing!
First thing I notice (granted I am still in the process of getting the save to load/downloading mods) is that the version you are using is still 0.6.3; that is, I understand not updating/changing mod versions mid-playthrough so as not to disrupt/break things, but with version 0.7.x I implemented a better means of event handling that did away with much of the on_tick processing, as the events would be scheduled instead.
The above is to say that in the mean time while I am still investigating, if you are willing to try updating to a newer version, I believe that should help at least some.
Unfortunately from my own testing at least, updating to version 0.7.4 did not improve performance as much as I would have hoped (dropped from a little over 0.6 to about 0.5. That said, I did find changing the mod runtime setting for "Number of surfaces processed per tick" to 1 appeared to half the performance cost for me from about ~0.6 to ~0.3 while still on version 0.6.3 - could be used in the mean time while I continue to investigate.