I followed two guides over at transformerprimeroot.com. One for rooting my transformer and one for installing ubuntu.
The process seemed to do weird things to my binaries though, and several commmands i didn't know it would do. One of them was cd /system/bin/ && chmod 4777
There are other problems as well:
Random crashes in gmail and other applications
Compiling helloworld and installing via eclipse causes a segmentation fault.
Starting a terminal emulator launches a shell with superuser permissions (i don't wan't that, i wan't to type su to do superuser stuff!)

I did a factory reset because i thought that would restore my system directory, but it didn't. Android Market crashed just a few minutes ago, and i still get a root terminal when running terminal emulator. Now i feel kind of stupid because i didn't take a backup or verify that factory reset did what i thought it would do.

Any tips on how to fix my system folder?
Could i download a dump and copy over the system directory, or would that cause even more problems?

 

Yes, it seems sketchy indeed. And only allows moderated comments. I should probably have seen the blinking red light.
It's the same guy as androlinux, that's where i found the guide.
It's the top hits on google for "transformer prime root" and "transformer prime ubuntu", though.

Anyway, here is the guide (it's for running ubuntu in a chrooted environment):
How to Install Ubuntu on Rooted Transformer Prime! | Android+Linux=AndroLinux

I haven't unlocked the bootloader yet, but i might as well do it.
Are there any disadvantages to flashing with another rom? Will I still get updates the normal way?

EDIT: typo

EDIT: If I download the firmware from asus' own web page, do i still have to unlock the bootloader?

 

How do i load the firmware? I tried holding volume down, then pressing volume up, but all i get is a picture of an android lying on it`s back. Can you please point me in the right direction?

EDIT: found out myself. Put the zip on the microsd card and inserted it into the prime. Android recongized the file.

EDIT2: Everything is back to normal now, i can even run HelloWorld
I installed version .15.