Accumulated junk can definitely make a big difference. Also, I never had electric fans, but at least on the MkIV chassis with 2JZGTE there are very few electric fans that can push as much air as the stock fan. Also, once you are rolling over about 20 mph, the fan is of little or no use to help cooling; fans help cooling when you are rolling slowly or stopped.
If your new radiator is not properly ducted, you are probably getting worse cooling than the stock setup. If you have a decent intercooler it's probably not a major factor although a poor design will be more restrictive of air flowing through it to the radiator.
This oil temp problem may not relate to your issue, but in my experience a 2JZ well into sustained boost will rapidly elevate oil temps to dangerously high levels. For an occasional highway pull you can get by, but for something like prolonged hard driving (like roadcourse track days) IMO you must have a large oil cooler.
I just ducted the air coming in through my front bumper so it can't flow around the sides, it has to pass through the FMIC and to the radiator. I am now also grabbing air from under the stock bumper where I have a narrow wide opening in my front lip and channeling that back to the radiator. This made a significant reduction in my water and oil temps.