Basically what you need to do is this if i undertsand you correctly
Spawn mobs -> delay or time call -> clear mobs
So this is what you do
#ACT
MonGenP "E003,40,40,30" Monkey 45 "noitem"
then insert delay or timecall
#IF
CheckMonMap "E003,40,40,40" 90 Monkey
#ACT
MonClear "E003" "Monkey"