Re: Many modules in the packages;
As this is a WM 6.5 ROM, this is both normal and expected. One of the big advantages of a native WM 6.5 Kernel is being able to use Slot 60/61 for Modules, freeing up space in slot 0, which is very important to the WM Memory Model
You can easily recmod the modules if you're on a 6.1 nk.exe.
The "not a valid pocket pc app" is a generic error, more than likely there is a .dll import that the package is dependant on, that you have not included in your ROM. (as ankit360 said it's probably a .dll in Manila2D)
I recommend a program like PE Explorer, in this program you can open up an .exe or .dll and view the Imports - if any of these .dlls are missing, the program will not function (as some of its functions are imported from that .dll, so without it, the program is broken)
Simply include the .dll's or the entire package that the .dll's belong to, and it should run fine