5.2.17 to 5.3.10 hosting site upgrade breaking things (depreciation errors)

[eluser]LouRocco[/eluser]
Aken -- Thank you. I saved a copy of the original files then went in and edited them. Your edits worked--I don't get those depreciation errors on load. But now I've noticed other errors (which we're probably always there). No matter where I click on the site, I get this error:

An Error Was Encountered
The URI you submitted has disallowed characters.

Any other advice on those?

Also, what is "CI" and how would I know what version?