Sounds nice to limit the search in certain category.. nice work! but what does this mean? "and stemmed words are penalized."
The stemming issue is reported in bug 2511 [*]. The bug is caused by the indexer not indexing the original word, but only it's root (i.e. stemmed word). Now both are indexed, and original words are preferred, i.e. have larger scores.
ps.. about search in categories, note that subcategories are not expanded, this needs to be done at client side (i.e. in mediawiki extension).