I followed
https://wiki.mobileread.com/wiki/5_x_Jailbreak and it did work.
The wiki page isn't clear for 5.8.9.0.1 (which you decided to use) so I'm not sure the directions / files are exactly the same as those stated there.
I think you had a problem with either step 6 (JB) as you didn't see the JB message or 7 (Hotfix) as once you upgraded your firmware it didn't seem to be jailbroken...
As I understand it (I'm no specialist, just another newbie!) you now can't downgrade to 5.7.4 or 5.8.9.0.1 to try to do another JB so you're stuck with your not JBed kindle. UNLESS it's jailbroken, but if that's the case I don't know why mrpi doesn't work: I had no trouble reinstalling my stuff using mrpi once I upgraded my firmware. Again, to me it seems like your device isn't JB or that you forgot to install the hotfix.
Good luck! (and at worse, you still have a working kindle, with calibre it can be used to read quite a lot of stuff!)