Transmission shudder advice

With that much mileage, I'd perform drain and fills, not a flush. There is in all likelihood varnish coating the clutch plates. If you suddenly replace ALL the fluid with fresh ATF, it will act like a solvent and dissolve that varnish in one fell swoop. Then you'd have shifting issues. Warm up your FJ and drain and refill with Toyota WS ATF. Measure what comes out and put the SAME amount back in. Drive and see how it shifts, then do it again and test drive. Do this 2 more times, but on the final time, overfill it just slightly, get the trans up to 130 F (borrow or purchase an infrared handheld thermometer to point at the pan), make sure you're parked on level ground with the engine idling and remove the level check plug and let the extra drain out until it's just a dribble and reinstall. The level check plug has a small internal hex like an Allen bolt. You may want to purchase the 2 plug washers and the level check o-ring and then install them on the last drain procedure you do.

The OP has twice that. The clutch plates in the transmission are almost guaranteed to be covered in ATF varnish. If that gets dissolved suddenly by new fluid, then you'll get shifting issues and clutch slippage. Better to do a couple of drain and fills and see how the transmission responds to the new fluid and work it in slowly. If no issues show up in 3 or 4 drains, drive it for awhile and then do a full flush. That, or just perform a regular drain and fill every year like you do an engine oil change as regular preventative transmission maintenance.