The problem with the Control Panel popup is that a 32bit Litestep can only show 32bit Control Panel entries. Which most of the things in 64bit Windows aren't.
That can be fixed by using a 64bit LS which, as it warns you on the page, can only use 64bit modules. There aren't that many modules built as 64bit (think this list by Alur is the most comprehensive list of 'em.) On top that, using the builds from '13 have problems with the xModules. (Or the other way around. It's because the xMods were built on an older Visual Studio with.. some flag or other set which makes them unloadable by LS which is compiled with a newer VS.)
As a workaround for the Control Panel issue you could just make an entry in your popup.rc:
*Popup "Control Panel" explorer shell:::{26EE0668-A00A-44D7-9371-BEB064C98683}
Which will just open the CP in an Explorer window. Here's a few other options, depending on which CP view you prefer:
Control Panel shell:::{5399E694-6CE5-4D6C-8FCE-1D8870FDCBA0}
Control Panel (All Settings) shell:::{F90C627B-7280-45DB-BC26-CCE7BDD620A4}
Control Panel (All Tasks) shell:::{ED7BA470-8E54-465E-825C-99712043E01C}
Control Panel (Category view) shell:::{26EE0668-A00A-44D7-9371-BEB064C98683}
Control Panel (Icons view) shell:::{21EC2020-3AEA-1069-A2DD-08002B30309D}
The nModules don't use the same config syntax as the xModules. You will need to adjust your .rc files accordingly if you wish to change to nMods.
And last, the fixes and upgrades to the LS core (and the nModules) aren't there to make 'em work on 64bit platforms, just so they'll work better with Vista and above in general. Including some stability fixes, rendering methods not supported by XP or earlier and taskbar entry thumbnails.