Improved system mods to 3" exhaust
Your Magnaflow pipe and muffler looks great. I imagine it helps with performance.
The whole 3" exhaust system idea would be greatly improved by removing the stock 2.25" exhaust Y joint just past the 2nd set of catalytic converters. It could be done by replacing the 2.25" Y with a 3" Y. The 2.25" Y section is the smallest restriction in the whole stock system. And this would retain the California exhaust standards.
Here is an illustration of the stock exhaust system parts. Click on the two illustrations for enlarged views and a parts list. Notice the Y section where the two pipes converge just past the 2nd cat.
2015 Toyota 4Runner Parts - TRDParts.com
The illustration, if this link works:
http://www.trdparts.com/media/images/oe/collision/8/8418270.gif
Any custom muffler shop could cut and weld transitions from 2.25" to 3" pipes and a new Magnaflow 3" Y before the pipe heads back toward the muffler. It's all very close so the conversion might also require moving the 2nd, left cat back a ways, or moving the Y downstream a bit, in order to fit the transition. Here are some of the required parts:
MagnaFlow Performance Exhaust - Pipes & Tubing
Another possibility is to cut off the 2.25" Y section and convert the two 2.25" pipes to two 3" pipes extending back to a dual inlet muffler from Magnaflow. Magnaflow offers several variants on their 5" by 11" x 22" oval muffler with 3" pipes; dual inlet/dual outlet, dual inlet/single outlet and single/single, which is what you have. The Y could occur past the muffler. The exhaust could be a 4.5" pipe (same volume) from the dual outlet muffler to the exhaust tip with a few pipe size transition and Y parts (past the dual exit muffler).
These larger pipe sizes occur on bigger trucks so why not adapt a larger exhaust pipe to a Toyota with a dual inlet/dual outlet exhaust muffler?
With this kind of enlarged exhaust system then an enlarged air filter or cool air intake might also make a difference in performance.