I don't really use RM2003, but I suspect the mechanics to be the same, so I will try to explain in XP terms.
1. Start the timer with an event, then turn that event off by using switch.
2. In another event, set up a parallel processing event that checks the items with conditional branches. (Conditional branch: If item 1 is present, then if item 2 is also present, turn on a switch or w/e you do when you get them both).
3. In the same event, do a conditional branch at the end, checking the timer: if timer == 5 min, then turn on the loosing switch or simply activate game over.
Make sure to turn that parallel processing event off with switch when the checking of both items is positive.