Scaling injectors bigger than actual
 

So I noticed that my fuel trims were all over the place with the stock latency and scaling, LTFT Low was about 5% and LTFT Mid was like -7%.

I made some changes and I've got them both to around -4% at the moment. But in order to get these numbers my scaling is 585 cc/min.
Is it normal to scale injectors bigger than they actually are? I'm assuming that they are the stock 560's at the moment, I'm pretty sure the previous owner didn't change them because the car was clean.

The stock scaling is 542, I never had to change the scaling of stock injectors, you might have faulty or aging maf sensor and/or o2 sensor, also check your fuel pressure.

well I don't have any idling issues, no issues with closed loop cruising, AFR's are good. I doubt it's the 02 sensor. The MAF I'm not sure but I had it apart a while ago and it looked completely clean, I'm not sure how else I can check it

what intake pipe and air filter ???

not sure of the brand but its a silicone intake pipe.
air filter is an Apexi pod which I've enclosed in a cold air box that I fabricated out of rubber, then I dropped out the ICS tank and put a pipe to feed air to the intake from the vent on the bumper.
So would these change the fuel trim characteristics?

I've never experienced that kind of issues on stock injectors as I haven't used any kind of aftermarket intake with stock injectors. But your intake COULD cause this kind of issues. Changing intake may drastically change maf readings and may require to alter injector scaling, latencies or MAF scaling.

After switching from APS intake to a cone filter with silicone hose and a diy cold air box\shield, my car started running super rich and I had to scale my FIC1100 (RON98) to 1083 scaling instead of 943 that I used before, to make everything work fine as it was before intake swap.

yes its possible

ok great, thanks guys, puts my mind at rest.