No. AnyRemote does not use Bemused server. It could emulate it to some extent instead. See for details.
It is good idea to update automake package. It needs to install automake-1.9 or above. But i hope problem could be solved just by executing automake -a
Make sure all needed development packages have installed on Your system. For example, if compiler could not find bluetooth.h header file, You need to install development package for Bluez. To determine which package is absent is not so hard. Just remember which file was not found by compiler, then open http://rpm.pbone.net/ or http://rpmfind.net and try to search package You need to install.
In principle it is possible to support any application with anyRemote. There are several ways to do that:
Well, different phones works differently, so it could happens. Try to upgrade to the latest version of anyRemote. Inspect /tmp/*anyremote.log file to determine the possible reasons of undesirable behavoiur. (Make sure You set Log=true and Debug=true in cfg.file You use). Also, make sure what version of Java Client is the same as version of anyRemote.
Drop me a letter and i can try to help. Of course, it will take some time :-) Please, describe the problem, specify phone model and version of distro You have. Also attach to the letter full log file (/tmp/*anyremote.log) as well as terminal output of anyRemote.
Definitely. Send me a letter with short description and attached cfg.file. I'll add it to the next release of anyRemote. One note: Your cfg.file should works with both anyRemote/kAnyRemote and should not call any external custom made scripts.