OK as the next step I'd suggest checking over the condition of the engine earth connections, there's a large earth strap that runs back to the chassis / battery earth plus a couple of smaller wires that run out of the wiring loom and are secured to the engine with ring terminals and small bolts
these latter items are the ECU specific earth connections for coils and injectors
I'd check the condition of the injector plugs / connections as this could be a lean misfire if an injector isn't firing properly - the best way to check this is with a 'noid' light
Then check all the connections to the engine sensors one at a time, remove each one and examine for signs of corrosion or damage and a squirt of contact cleaner ( not WD40) will also help.
This could be an airleak after the airflow meter, any air dragged in here isn't 'seen' by the ECU and so not compensated for and leans the engine out causing rough running.
Check the hose clips for tightness and inspect the trunking for any cracks or splits and also all the vacuum system, the small bore pipes and fittings for cracks and missing parts.
The best way to locate a leak is to have the engine running and warm and then spray lighter gas around each joint in turn. If the engine rev's up you've found your leak.
Work your way through each possible joint one at a time and you should find it. I use a slightly flattened piece of brake pipe and some rubber hose from the can of lighter gas to provide a spraying 'wand' and allow a direct blast of gas into each area, especially those difficult to reach with large implements.
It’s also worth getting the fuel pressure checked as if this is low due to a blocked filter or faulty regulator or even a poorly pump will all result in insufficient fuel being delivered to the engine