ok looks like its booting ok....
--------------------- MERGED ---------------------------
booted all okay but first im going to try this:
Yep that can be done any time you dont have/cant load molecularshell.
Note that it will also recreate the ux0:tai folder (you need to delete it) and it will reset your ur0:tai/config.txt to default (back it up or set it up again after).
If you dont delete ux0:tai and you reboot, taihen will use ux0:tai/config.txt instead of ur0:tai/config.txt which we dont want when using an sd2vita.
Edit: it does work, I've used it to reinstall molecularshell before on a couple of different vitas. Make sure you hold R just as the black molecule screen loads.
If all your bubbles are missing (games etc that were on the vita mem card) not just molecularshell you have a problem with the microsd setup.