What diagnostics did you do and what was showing for injector 1, then 1,3 & 4.
The in tank pump would affect all injectors, but may be worth cleaning the strainer there. Likewise the tandem pump would also affect all injectors.
Could be an issue with the injector loom, worth checking the connections, or replacing the loom.
My daughters Golf MK5 PD had a rough running problem - the cam position sensor was bad so a new one resolved that issue.
If you can't fine anything obvious it may be worth pulling the injectors and seeing if any crap has got past the filters and is fouling the inlets on the injectors, easy enough job, just get some new seals and injector bolts. I've got printouts for the job if you need them.