Seph,
I pm'd you back. I don't know how long "a long time" was for the boot up for you but if it was only a few minutes you might have jumped the gun.
The problem with the 1.1.3 jailbreak is that it installs a huge (by comparison) flash image into your memory. I think it's like nearly 200 mb. (You only have 300mb to begin with. This is not your memory/storage you see when connected to Itunes...your "xx" gb available.)
That's why when you start, they tell you to turn off the autolock. Mine sat in what looked like a frozen state for over a half hour once while loading a file that size.
Once you get it running again, I'd advise using Bosstools to relocate some of your things such as fonts, etc. because you'll have very little space for the better 3rd party apps.
You can try this as well:
Connect your ipod to iTunes, and try holding the home and sleep buttons until the ipod restarts, then as soon as the screen goes black, let go of the sleep button. From there you can restore your ipod.
I just thought of this also...
What version of iTunes are you running? Some of the newer ones above 7.5 have "bug fixes" which disable oktoprep as far as I've heard. I jaibroke mine before these updates so I can't confirm nor deny but you might want to downgrade your iTunes and see if that works.
Last but not least, it might have to do with that .jar file you loaded in through SSH. 1.1.3 sets up its folders to run differently in the sense that most files ran from "/root" in previous firmwares where a lot run from "private/root" now or something along those lines. Which means your .jar file might be trying to load the wrong directory.
Have you tried to SSH back into it even though its frozen?
Hit me back through pm if none of this helps.