i have twin 700s in my boat and the one side is lagging in rpm at same throttle position by about 3-400. Leak down test is all good. No codes or warnings being thrown. per vessel view that side is burning about 2-3 gallons less fuel per hour than the other side at 4k rpm. Props were just reconditioned about 5 hours ago and show no damage.

Any advise on how to diagnose what could be happening. Could it just be coils, spark plugs and wires?

I'd say you are down a cylinder on that side. Check wires/plugs. Could also have an injector not firing.

i assume starting with just replacing wires/plugs and see if that fixes is best way to find out? Will injector not firing throw a code?

Have you hooked a scanner to it or just reading V-V

Edit: also check fuel pressure

All i know right now is it is it wont run at same rpms as other engine throughout the rpm range. Will scanner tell injector or ignition issues? I assumed V-V would tell me anything that a scanner would tell me.

I had 700's and had the same issue. Although it was not readily apparent other that I noticed a slight change in the exhaust sound. The coils will not show on the computer as not firing. The computer shows a signal sent to fire but does not know if it did. Mine ended up a bad engine wiring harness after testing everything. We also swapped coils around. It took lots of time to troubleshoot that one......

Was it an igntion harness? Did you also see the rpm difference between the engines?

I think with a scanner you can invoke a cylinder miss fire test with the 555 controller to see if all is well or may point you to a particular cyld.......... have you tested the fuel pressure ?

Years ago, I had an issue with my pair of 496HOs where one engine was always lagging by 300-400 RPM. It turned out to be a bad Crankshaft Position Sensor. The CPS can start to go as such can start go bad as such before throwing out error codes.
That would be something I would replace just for good measure. They are fragile, so not sure I would try swapping them.

Blower belt slipping??