Daniel,
I'm guessing that you are having problems with the grade for the toilet, therefore the act of elevating the toilet and cutting a portion of the hub on the 90 el fitting.

1) Normally the 90 el at the toilet flange would be a medium bend 90, either hub , or hub x spigot. When I have required even less space between the floor and the centerline of the pipe, I have used a 4"x3" spigot 90 el fitting with a hub 4" closet flange. This will reduce the centerline measurement down to 3-3/8" inches. Some trimming of the hub flange to fit over the curve of the top portion of the pipe may be needed to reduce it that much.

2) If the height of the toilet is important, keep in mind that seats can be bought with a variety of thicknesses.
In addition, toilets themselves come in 10", 14", 15" and 17" inch heights.

Regards,
Terry