Time out error
 

Coach is yelling what I thought was time out. I grant a timeout. Turns out he was giving instructions to his players and doesn't want the time out. I get ready to get the ball back in play with a throw in. Caseook 5.8.3e covers this situation pretty well, however now both teams want to substitute players. Is this allowed? Rules book citation appreciated.

Yes (assuming NFHS rules), look at when subs are allowed. They are allowed during dead balls (an IW qualifies as a dead ball), and there is no exception in high school.