Old boy blew a head gasket in his daily ef so we picked up another motor and dropped it in though we are now having problems with it.
Before we removed old motor the car was running fine besides the head gasket issues but now the motor we dropped in is playing up.

Problems are:
Massive miss and no power under load when accelerating more than 1/4 throttle
Popping in air box when over 1/4 throttle
Air box is sucking louder than before

We have changed:
Plugs, leads, coil, isc, tps, map, injectors, vacuum lines all off the original motor that had no issues but still no change.

Need to get this sorted cause its his only car ATM as he is rebuilding his el xr8.

Misfire and intake popping can be caused by running too lean - ie, too much air and/or too little fuel. I would be looking at:
- vacuum leaks around the intake manifold or in any of the vacuum hoses coming off it. Spray brakleen along all the hoses, gasket joins, injectors; revs will surge if you spray a vacuum leak.
- fuel pressure regulator.

Also, is the catalytic convertor OK? I had similar symptoms with a blocked cat years ago.

Did you touch the cam, cam angle sensor or crank angle sensor? Incorrect timing can cause similar issues. If you pull the fault codes, it should show if there is a faulty sensor.

Some areas to look, anyway.

Will double check over all vacuum lines, will carby cleaner do the same as brake cleaner making it surge? Will be replacing O2 sensor and fuel reg next to rule them out.

The cat is good, covered it up the whole time during the engine swap so nothing could get in there.

Haven't touched any of the timing or sensors, starts pretty good but has the miss with throttle so I think it's to do with air/fuel mixture so will have another play and see what I can find.

Carb cleaner will likely not work properly - too slow to vapourise and burn. Brakleen is far more flammable and volatile, so revs flare immediately when you hit a leak. It has worked for me when other flammable sprays haven't picked up the leak.

You can test the O2 sensor by simply disconnecting it. The engine should run fine without it, but it will run continuously in open loop - working solely from the ECU fuel tables, with no correction from the O2 sensor. Falcons normally run rich on the factory fuel tables, so you should get no misfires or popping with the O2 sensor disconnected.

When the engine is playing up above 1/4 throttle, do you get black smoke out the exhaust?

A real long shot here: A worn exhaust lobe on the camshaft will have similar symptoms. It's rare, and unless you have been messing with the camshaft, is extremely unlikely. The cam lobes are hardened only microns deep. Once it wears through and exposes the soft metal underneath, the lobe can wear completely off in a few hundred kms, and the exhaust valve doesn't open at all.