here's a good way to add in those after flash xml's and cabs, and mortscripts like to add back my game shorcuts to the start menu. the first one goes in your oem/tp2/common folder.
the other one is an example of the type of files that can be included on the root of the storage card. you can include it as is the first time as a text to make sure it works. I can verify it works very well. As long as the folder is named as is (XDA_UC), and put on the root of the storage card it will prompt you it is ready to run after flash and first auto reset. then it will tell you when it is done so you can soft reset. Here is the thread I got this from:
http://forum.xda-developers.com/showthread.php?t=562568
this handled all my cabs that didn't want to cook in, esp. good for the ones that require prompting because you can press ok, or enter info during install.