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Try go to Liberty Toolbox > Tweaks > Misc. > Mount System Read/Write.
Reboot system, and try install again. May or may not work. Also if you use Amazon apps, be sure to remount the system as read only, otherwise some apps may quit working and need to be reinstalled.
I had some trouble with that as well - and I actually have had that issue on several ROMs - normally what I do is just download the flashable zip and flash in clockwork. It's here Superuser - so I would suggest doing it that way. I can confirm this works on GB v.7 and v.8, and MIUI but no difference, it will work.
Nope, no need to mount anything. Just throw it on your SD Card, reboot to CW, install it like you would any other ROM. No need to clear cache or anything (at least I didn't and it worked just fine).
After you flash it you may have to go in to the SuperUser app and update the SU Binaries. But thats about it. No probs. I get annoyed when stuff won't update in the market, and I usually keep the SU zips on my server for situations like that. Used to happen on my Droid 1 all the time because I was flashing a different ROM every week.
I think has to do something with signing by the way, so the ROM may be to blame, and it's most likely because it's a beta - I already put this on bug reports as well, though it may more be a bug with the market version of SU.
Try downloading the superuser update fixer and run it and then update to new version of superuser. The same dev that developed superuser developed update fixer.