I have some (probably not very positive) answers, but here goes. In general Seam 3 is "as is" and will not be patched, improved, or otherwise changed unless the client (or another community member) wishes to do so. On top of that, patches submitted will probably not be merged or released since the last release was over a year ago now at this point if I am not mistaken. You'd have to find a committer who is willing to dredge this up again :) I'm not saying it's impossible, but there will be some pretty serious barriers to getting improvements made.
Aside from that, I believe Seam 2 is still a supported Red Hat project (Seam 3 never made it that far.)
1) You can try your luck with upgrading to Seam 3, but know that would be upgrading your customer to a project that is officially cancelled and will not be continued. There are still quite a few known bugs that were never fixed. Errai is still actively developed and has a good community. JAX-RS is a standard, and will be around for a long time to come, so I would probably echo what was said on the list. That being said, there is good in Seam 3, and a lot of good work went into it, so if you are OK with the circumstances around this project, then I would say continue at your own risk, but you may find it works.
2) Look at the CDI conversation scope with JPA and an @PersistenceContext(type=EXTENDED) context. This is effectively the same thing as a Seam-Managed Hibernate Session, except it will not be closed and re-opened before/after RESTORE_VIEW phase. However, you can use EJB @TransactionAttribute methods to do your work in a transaction where required. (See this article for more info on that:
http://ocpsoft.org/java/spring-to-java-ee-a-migration-guide-cdi-jsf-jpa-jta-ejb/ (The article is about Spring, but many concepts are shared with Seam 2.)
3) There isn't really a good XML configuration mechanism in Java EE (other than the basic web.xml, persistence.xml, ejb-jar.xml, etc...) So I don't really have a good recommendation for you here.
New questions:
If you are looking for functionality to control Routing and Navigation, check out
http://ocpsoft.org/rewrite/ (with the rewrite-integration-faces module) or
http://ocpsoft.org/prettyfaces/, which includes both of the former - either of these projects will give you access to several utility classes such as the "Navigate" class, and other things, but all said, JSF2 has much better support for navigation than JSF 1.2 did (which is what I guess you are using if the customer is still on JSF 2.2)
I hope this is helpful, but I do wish I had better news. I would really consider Errai or just plain Java EE with JAX-RS. I can't really recommend that anyone start using Seam 3 now, several years after its demise.
~Lincoln