Synner, then it would break the normal hacking rules.
I have obvious bias as I'm in this party. Although I'm neither the dead guy with the timer nor am I the guy with the bomb in his head.
I would do it by first thinking logically about how the process would go down from a business standpoint, that way the run makes sense. Once you understand how the process is going to work it becomes easier to make a run out of it.
Picked on Elven Street Sam gets access to the two unconscious mages who attacked him. They're unconscious because a totally awesome Orc wasted them both in one round with stick and shocks BTW...
*speculation on my part*
Elven Street Sam calls up fixer and says he'd like some insurance in the form of a cranial bomb. He'd like it done soon and pays extra. Fixer calls up the mob or some criminal organization that does this. Probably a criminal organization as they like blackmail ops and cranial bombs are awesome that way. The contact their own doc's who implant the device. They also take DNA samples and cross check with SIN's to know who they're pissing off.
I'll go on the assumption that his is all done fairly professionally and organized on the other end. They need to watch over their charges of course and getting the bomb probably includes some monthly fee for continued maintenance of the bomb. As well as safeguards that the guy will be dead It's basically a contract on his life that hasn't been activated yet. And loots of nuyen buys a lot of insurance. The information is entered by the mob who passes it on to the doc and monitoring company. Once it's there they keep a wireless watch over the cranial bomb when it activates every day at a certain time. They also download the information onto a data chip and take it to a wireless of non-matrix node where it can be monitored by RL people to cross check with the online data. They know that people with bombs in their heads will usually try to contact a hacker and it helps having a non-matrix backup to compare to from time to time.
Post implant procedures:
Every day at X time the device activates in hidden mode and looks for a code to detonate or get regular info. Lets assume it doesn't automatically detonate if the local node is down and that there are built in safeguards to avoid killing that prized prostitute you want to keep loyal just because she was in an area with no signal.
If it misses a signal one day a computerized notation is recorded. People check the log for these from time to time. If a second signal is missed it informs a RL person (sends an email to the on-duty person). That person checks other records (matrix searches, etc) for that persons info. If they had his DNA and SIN they could search for him being at certain restaurants, etc. The on duty operator would also maybe call the person that paid for the service and inform them that it's been two days and ask for further instructions? Maybe trying several times to get a hold of them even. If the person was in danger of their life as in this case they probably left instructions on what to do in the event of their untimely demise.
A third day comes and they dispatch an investigator to check out the situation. They look at the guys place of residence or known hangouts and look for recent activity. There should be a record of where he is every day at X time which gives the investigator a solid lead on where to work.
Now if they still can't get a hold of the guy with the bomb they probably have rules. In this case it's to blow him up. I assume they send a signal to detonate and get some sort of confirmation signal back. Perhaps even send someone to investigate or witness first hand? If that doesn't work because of some jamming I assume they watch known hangouts and put a bullet in him with a rifle from across the street, car bomb, poison his drink, or something else.
The run:
Guy who set it up is already dead. Hack into his comlink and get the information on who was contacted by home. Get a receipt for the Waterworld Surgery (big bomb!) with a Enemy of the State surveillance package (continual monitoring), and the WD40 backup plan (grease him!). Matrix data searches to find out what type of bomb and what will happen at the various stages.
Wireless hack into the device the first day to try to shut it off or temporarily spoof the signal saying everything is normal.
Bribe/threaten a street doc to remove the device after that.
Get info from the mob or hack/data search to find out the physical location of this monitoring facility. Break into it and edit the offline backup so it can't be discovered later. Or burn it to the ground capturing all the codes and possibly sell that data to another mob or blackmail those people yourself. Or detonate them in a mass killing spree…
If you're too late and alarms are triggered you'll also have to fight off the security teams at your known hangouts or other places.
At the very minimum you've managed to let it be known where your hangouts are and pissed off some shady criminal organization. At the worst your brain is charcoal.