Sorry to hear that you got a lemon 1zz motor in your Matrix.
I hope you were under warranty to have the issues taken care of.
I have never heard that the same car can have a spun bearing & a thrown rod, unless it was boosted with some Forced Induction power addder and even then not many have had the issues that you had.
Correction to your post though. The 1zz motor is Toyota's own which I believe is made in Canada (IIRC the Vibe & 9thgen Corolla are made in California) & the 2zz motor is Yamaha made.
To convert your 1zz Matrix to a 2zz powered one would require:
different motor, different tranny, different ECU, different shifter assembly, and a different gauge cluster.
It would be very difficult & very expensive, but it can be done I suppose if you throw enough money on it.
It would be more cost effective to get a new 1zz-fe motor, and if you want more power - get a TRD S/C or perhaps go turbo.