When you followed the advice above, did you replace emacs-i386 in the commands with emacs-ppc? You need to do that, otherwise it won't work. You need to delete or move /usr/bin/emacs-ppc, then run 'sudo /usr/libexec/dumpemacs -d', then it should work. If it doesn't work, please paste in the output of the dumpemacs command.
X11 on Leopard has many issues, because they upgraded to a new version of X that didn't have many of the patches Apple had previously applied. To solve the multiple items in the dock problem, what you have to do is not launch X from the dock. In this version of X, it launches as soon as something tries to connect to it. So instead of launching it from the dock (you should just remove all of the icons from the dock), you can launch it by just opening any program that needs to use X from the terminal (make sure you don't override the default for $DISPLAY in your .profile or anything).
For your issue with your IDL, you might want to try recompiling it with the current version of X. Other than that, you may have to wait for Apple to release a version of X that fixes some of the bugs. If you'd like, you can try out pre-release versions of the X server that fix several problems; they may or may not fix the problem that you're having:
http://wiki.x.org/wiki/XDarwin
And for tcsh, you need to go into System Preferences, choose Accounts, and click the lock and enter your password. Then, right-click or control-click on your account name, and choose "Advanced Options..." from the menu. Then you'll get a screen where you can change your account's shell.
