For item 1, I'm not sure what type of server you're using. You mention in step 2 that you are using a jboss 5.1 server type and it works. What type were you using in step 1? The only server types which supported esb 4.9 are JBoss AS 5.1, 6.0, and EAP 5.x. Other server types do not support the esb 4.9 module.
If you were using the deploy-only server type, that one also did not support esb 4.9, but, I've opened a jira and committed a fix to that. (https://jira.jboss.org/browse/JBIDE-7743)
For item 2, what do you mean the publishes aren't showing up on the server? Are the class files actually being changed in the deploy directory? Has the timestamp changed? If the timestamp has changed, Typically runtimes do not accept changed class files without restarting the module. You can do this by right-clicking the module in the server's view and selecting FULL PUBLISH. Only seam applications accept hot-code replacements without a module restart, and web projects do too for changes to jsp files or static html / xml files.