Hmm... ok, I don't mean to be rude in saying this, but you disabled the single best-proven SEO extension for Joomla based on "expert" advice, now you're worried about SEO problems JoomlaComment is causing....?
I don't really see the logic in that
What's wrong with sh404SEF? It's an absolute beauty of a thing - as long as you configure it correctly and are prepaired to change things with manual aliases...
Anyway, i'm going to give you a hand here and address all the XML errors I can see
XML Parsing Errors
Line 154: Turn off the 'Write Comment' link for a quick fix, and use the 'Read More...' default instead.
Lines 294 + 295: That is being caused by the cbLogin module which is known to be not very valid. If you don't already have the latest Community Builder installed (1.2.1) I highly suggest you do so as CB 1.2 is easily hackable (you should of gotten a security bulletin from Joomlapolis). Regardless, chase that up with them on the Joomlapolis forums or fix it yourself. Something to do with closing tag order being wrong
Line 479: There appears to be a missing paragraph close tag there or maybe two missing </p> I can't really tell what's causing that..
...all the other XML Parsing errors I think are caused by the same things, missing closing tags or being closed in the wrong order.
general entity X not defined and no default entity
Line 154: Again caused by the 'Write Comment' link. Is this 4.0 Beta 1? We can work on fixing the validity of that for the next version (4.0 RC)
Everything else... well its all related. They seem to all be caused by either "Write Comment" and/or the CB Login module. Try turning both of those functions off temporarily to narrow it down a little bit, run the validator again, and paste your results in a code box here
Using the process of elimination is a good tip when trying to nail validation bugs. I always run the validator whenever I add a module or extension or change any structure.