Whodunit...where should I put it?

That's entirely up to you. But, I like to believe that starting something while a scene or action is already in motion is a good way to go. In other words, enter the scene at the end and go from there.
Just some thoughts for you. Good luck!

My spontaneous feeling is that you want to write a thriller and that the detective part of the novel is secondary. That is because most of the action happens in the thriller part and you don´t seem to know what to write in the detective part. I am afraid that the death of the MC and the shift in perspective will stop the momentum of the story so that everything that happens afterwards will be uniteresting to the readers, especially since they already know who the bad guys are. To put the detective story part first would not be very satisfying either because it seems to contain less action than the thriller part and also that would make the thriller part less interesting to read because the readers would know that the MC will die in the end anyway and they wouldn´t be as interested in his survival.

My suggestion is that you concentrate on the thriller part and maybe you can put a short detective story at the end, like an epilogue, so that the death of the MC can be avenged and the bad guys punished. Maybe the MC somehow deliberately left some clues to the detective so that the bad guys can be arrested. Maybe it would also be more interesting if the detective finds certain facts or conspiracies that the MC did not know about.

But that was only my opinion. Of course you know best because it is your story.

You know I was reading this great book that I never finished called "MY NAME IS RED" which begins with the chapter "I AM A CORPSE" in which a narrator is dead but is narrating from beyond the grave. The book then goes into various other narrators like "I AM A DOG" and "I AM A TREE" and "I AM THE COLOR RED" etc. You can use this technique to have your MC who is dead narrate from beyond the grave so you won't have to have a major POV change. Just a suggestion. Trust your insitincts though. And remember to use the spell check... er... force.

You know I was reading this great book that I never finished called "MY NAME IS RED" which begins with the chapter "I AM A CORPSE" in which a narrator is dead but is narrating from beyond the grave. The book then goes into various other narrators like "I AM A DOG" and "I AM A TREE" and "I AM THE COLOR RED" etc. You can use this technique to have your MC who is dead narrate from beyond the grave so you won't have to have a major POV change. Just a suggestion. Trust your insitincts though. And remember to use the spell check... er... force.

***Spolier warning***
Actually I have the book My Name is Red in my bookshelf, borrowed from the library and Im interested in reading it if I get the time and lust to do it. Earlier I read the novel Snow by the same author, Orhan Pamuk. I liked that book but the worst thing about it was exactly that the narrator tells early on about how the MC in the end will fail and live a lonely, depraved and worthless life and be killed in a meaningless way. That took away a lot of my interest in reading any further, but I read it to the end anyway because it was good overall. Thus I don´t think Pamuk is a writer one should try to mimic when it comes to this kind of thing. In my novels I never warn the reader beforehand what will happen in the end or if the MC will die or not because I think it makes the novel more thrilling if you don´t know. The best effect I think is if the death of the MC comes as a shocking surprise for the reader. But that is only my opinion.

I'll keep it short and sweet:

Why would a reader keep reading if he or she already knows who did it, and why and how?

Where's the mystery? Where's the intrigue?

Where's the fun for you as the writer?

Simplest solution: Stick with one POV, the investigator's; put the murder at the beginning of the book, turn the investigator loose and let him or her dig out the truth.

All those action scenes you planned for your victim can easily be switched to the investigator. There's no reason why hired guns wouldn't go after him/her, even if he is officially a cop. Of course, the best assassins make a killing look natural. So, in this case, the cops might not even realize that a murder has taken place. Maybe the family hires a private detective, or the man's insurance company, or maybe it's a relative who gets suspicious.

Back to my main point. If you dwell on telling the reader EVERYTHING -- who did it, why they did it, etc. -- then there's nothing left for your investigator to find out, and no reason for the reader to keep reading.

If you want to write the action story you describe, and still kill off the MC, you might want to have the whole story witnessed by someone, or have the documentation of everything the MC knows sent to someone, so that the perpetrators can be caught. Then, you can have a relatively short epilogue showing how the bad guys got caught and punished. You can reveal in the epilogue that the narrator is actually the one who witnessed everything, or received the documentation, and he/she is being debriefed about it all.

You can also write in third person omniscient and avoid the POV problems.

Why do you want to kill off your MC?