MK1 VRS 2005 Hesitation and back fire

Hesitation around 1-2k and 3-4k rpms. Occasionally back fires. Rough idle

Using a good car without issues as a doner we have changed every sensor possible, coil packs, ecu, fuel pump, new fuel filter, new plugs, compression checked. As far as we know the timing is correct but will check it. No fault codes, nothing found in live data with VAGCOM. It looks like the previous owner has been playing with it as the air box has been removed in favour of a induction type, turbo recirc valve has been replaced with a forge one, vac reservoir tank is removed and the pipe blanked and vac pipes and secondary air system had been partially removed (I get the feeling the guy wasn't sure what he was doing), we believe it has a map on it but don't know whos it is. I think I have either a air leak, unmetered air going into it or we are over fuelling, failing that a timing or ignition problem. Im looking at replacing the wiring harness for the coil packs as it does not look the best condition with a split insulator on one of the wires for cylinder 1 which I have taped up but don't believe it is all down to this.

We have got the car to this point which was hesitating through all the rev range and wouldn't idle to start with by replacing the relevant parts that made a difference from the doner car and a lot of trial and error.

Any ideas appreciated.