WoW! Lots of issues here with your production techniques.
Not only are your markers colored wrongly but they compound your issues by having been erroneously placed such that they cut into your foreground characters.
As for your post correction on stabilizing, take a look here – https://library.creativecow.net/articles/swanson_grant/Final2_mixdown2.php
Do take note that you will have to rotoscope out the markers, which isn’t covered out in the linked tutorial. The rotoscope requirement isn’t too difficult if you cut some slack on the edges of the hair but it’s still a lot of unnecessary work!
Now, back to your main issues, which involve production techniques and values. Do set aside a budget for an, on-set VizFX Supervisor the next time you venture out on a VizFX job. This shoot was done without an idea of how to piece things together in post and that’s a disaster already in the happening. ‘Fix it in post’ is bad enough a thought, even when a solution to how to fix it in post is known.
The COW’s job forum and your own contacts will allow you to link up with folks that will not only do the job but allow you to assimilate some useful knowledge/tips while on the job.
HTH
RoRK
Intensive AE & Mocha Training in Singapore and Malaysia
Adobe ACE/ACI (version 7) & Imagineer Systems Inc Approved Mocha Trainer