Yes, there's a way to confirm ignition timing. You need to locate top dead center then mark the PTO wheel accordingly. A piece of wire clamped under a rear screw and bent to match the TDC mark serves as a temporary TDC pointer.
You will use a piston stop to locate TDC or preferably a dial gauge, through a plug hole.
These are temporary references b/c the PTO is threaded onto the crank and can move over time, it's not keyed.
It might be easier to consider how timing could've been disturbed and correct that b/c to change timing parameters requires reprogramming the MPEM TDC offset.
It;s pretty easy to overlook disconnected harness connectors, and a couple of them are easily swapped mistakenly.
I wonder if you just have fouled plugs or a fuel issue?
But considering you're working on a DI, it's important to have the factory service manual in hand b/c it's worth it's weight in gold concerning detail of the various diagnostic procedures.