Get the serial number of your machine, go to the Scag website, click on manuals on the left, click on STT, find your serial number group, click on the parts manual. It will download as a pdf and toward the end of the manual are the wiring diagrams, print out the one that has your engine.
Generally when fuses get hot there are several causes; the voltage regulator in the regulator/rectifier is letting the voltage get to high. With the engine running at half throttle or more, the voltage across the battery should be not more than 14.3 VDC. All battery power passes thru the key switch and several connectors along the way, all of which are subject to high resistance from corrosion and dirt. The charging system output is also controlled by the keyswitch and when in the off position, the charging system is isolated so battery power won't back feed and drain the battery. Keyswitches are known to go bad. As has been mentioned, chaffing of wiring is always a possibility. Battery ground connections which are generally connected to an engine mounting bolt are another possible problem source. Why did you install a new clutch? Have you needed to recharge the battery between machine uses?