I just retested with and Firefox 4.0, Chrome 10.0.648.204 and Opera 11.01. Most of the errors are still there, some of them even worse:
* In Opera when clicking on a namespace in the file tree, the whole page (i.e. the ACL manager) gets loaded as a sub item.
* In Firefox and Chrome the TOC doesn't even show the toggle arrow. (Which is definitely a JS issue, because the whole markup for it is missing from the TOC header.)
* The sitemap/index behaves even more erroneously than before.
I haven't tested too extensively. (Otherwise I'd probably have found more bugs. ;-) )
Yes, I agree that fixing these issues don't make sense until after the jQuery rewrite. I'd still leave this bug report open, but don't agree that it should be "Due in Version: April 2011 release". After the jQuery rewrite is done, these issues (and probably more) will need to be re-tested anyway.
As for the align attributes, see FS#1351