Vitashell can just be re-installed using any of the exploits again. Actually, it's somewhat recommended you have Vitashell both in your Sony Mc and also in your SD2Vita location; that way, if for some reason your Vita boots without loading your SD2Vita (faulty SD card and/or adapter), you will still have access to Vitashell, which makes fixing your issues easier.
So, you need to re-install Vitashell (use the exploit you used in the first place to enable HENkaku and download Vitashell again, assuming you still have it), then use Vitashell to change your config.txt so everything points to ur0:/tai, and place every plugin you use, along with the config.txt, in that location, too. If you have it, delete the whole ux0:/tai folder afterwards as you won't be using it.
Reboot afterwards, and everything should work properly if your config.txt is correctly setup as mentioned before.