Make sure you get the latest driver updates (the
hoot-ini.zip on snesmusic.org). If you do, you should have a "doujin.xml" file under the xml folder. As for the rest, just put the thxx.zip files in the pc98 folder, and the YM2608 drum samples in the main hoot folder. If it's all working okay, when you open hoot, it'll scan through everything and show the Touhou music under a "doujin" category.
One thing you have to remember, the PC98 came with two different "official" soundcards, the "26k" with a
YM2203 soundchip, and the "Speakboard" with a
YM2608 soundchip. The YM2203 (a.k.a. OPN) has just 3 FM and 3 PSG channels, while the YM2608 (a.k.a. OPNA) has 6 FM, 3 PSG, 1 general-use ADPCM, and 6 "RSG" percussion channels (the drum samples). The earlier PC98 Touhou games were written only with the 26k soundcard in mind, so they'll only support the YM2203. Mystic Square supports both soundcards, and includes YM2203 and YM2608 remixes of the music from the previous games. So you'll see different versions of the same game available in hoot, each will sound different. For example, HRtP should have "Original Version", the original HRtP music for the YM2203; "TH05 Version (OPN)", the Mystic Square remix for the YM2203; and "TH05 Version (OPNA)", the same remix for the YM2608.
Hope that helps. =]