Hi,
Sorry for the delay. AWP can work with your GSL, AWL and AVL lists and provide lemma information assuming the lists contain this information. If you POS tag all your raw data files and provide lists which also include POS information in the same form as the raw POS-tagged files, AWP can deal with POS information, too. However, you will need to set up the raw files and the lists in advance to do this.
I suggest you play with the software on a few tiny files and lists to understand how the program works.
AWP should certainly work fine with 804 files. When you say it stopped working, did you wait long enough for it to finish? Again. try a few small files and then simply copy and paste these into the same folder until you get to about 1000 files, and see how long that takes to finish so you can estimate the process time. I suspect the problem is that some of your 804 files are not UTF-8 encoded.
Laurence.