Hi Andrew, IIRC it took some work to get search crawling up and running. I'll check my test lab here and get back to you on it.
Your other issues may or may not be related to AAMs. You say you are using split DNS-are you using two VIPs, one for each DNS zone? Have you tried configuring the iApp to not use any caching, compression, or OneConnect profiles to see if that helps (not that we'd do that permanently, but it would help identify the issue).
BTW, the SharePoint RC3 iApp was promoted to downloads.f5.com. I recommend using that one because it's officially supported.