You people are getting confused...
There a two clocks: The Wall Clock (above the mainframe) and the Link Clock (30 second timer to link the teleporter)
The Wall Clock shows the time Dr. Maxis (Rictofen's Master, and voice during dog rounds "Fetch me their
SOULS!) was trapped in the alternate dimension (dimension where hell hounds come from). You can activate the Wall Clock by shooting it with an Upgraded Wunderwaffe.
The Link Clock is simply a 30 second timer. You can use this as many times as you please until you link all three. You do NOT have to link all 3 to use a teleporter (you just must have linnked the teleporter you are attempting to use). All linking 3 does is unlock the PAP machine, and give the ability to activate the fly trap. The Link Clock has nothing to do with the mystery box, Wunderwaffe, or Monkey Bomb,
I am unsure if the wall cloack does, but I don't believe so. (I got the Monkey Bomb AND the Wunderwaffe back to back during round 5.)
So...the Wunderwaffe won't be going anywhere until someone figures out how to release DR.Maxis from the alternate Dimension.
Hope I cleared some things up
-Rann