I do have 12 holes in two XJs, a '98 and an '00. I also had Ford 4 holes in the '98. Also, had another '98 with 4 holes. On both '98's the 4 holes did not seem to add any power by the but dyno. The engine did seem to run smoother. I also, did not see any MPG increase.
On the '98 that I changed to the 12 holes from 4 holes, it was running rough. I mean really rough, and down on power. When I changed to the 12 hole, the power increased. I mean noticeably. Then it kept getting less and less. After a week, it was back to as before. I did replace the spark plugs. I had Champion Truck plugs and replaced them with NGK. Or I might have used some new Champion Truck plugs. The '98 ran about as stock.
A guy who I have do work that I can't handle, mainly welding, also said he had the same experience. He racked it up to poor quality of Chinese stuff. I bought one of my 12 hole sets from Cobra Marty. The other off of EBay. I also wonder if the ECM is adjusting parameters back to 'stock'. ???
On my '00, I was battling to get it to start. The plastic case of the stock injectors were cracked. So, I used some 12 holes off of EBay. It runs about stock. I did run the engine several times before driving it. So, I would not have noticed if it gave more power and then adjusted back to stock.
Also, there is more to injectors than the number of holes. Some say the Neon Injector has an 'Advance' hole shape, with its single injector.
As stated before there is the impedance and also the rated pressure for injectors. So, I wonder about having the EMC reprogrammed and the fuel pressure increased. I am going to try that possibly latter in the year on my '00.
I would also check your plugs. I'd probably go with NGK. Did you change the O2 sensor? With NTK or MOPAR? I did change mine with a Denso. The one replaced looked rough. Also, I don't think it was tightened in correctly, or a bit lose. Still, I saw no real improvement. I do have an intermittent miss. I do have NTK O2 sensors to put in.
Don't know if any of that helps.