One of my bushings is toast after only 25,000 miles. They may be OEM style, but they certainly aren't OEM quality. I'll be replacing the bushings with genuine Toyota parts.
As I inadvertently learned today that the wiper and defroster are disabled if the window is not fully closed. Possibly it's not correctly sensing that the window is closed or something is in the upper track that is keeping it from fully closing.
Just get a cheap angle grinder from Harbor Freight, put a cutoff wheel on it, and cut out the part you don't want. Faster and cheaper than paying some shop to do it.
You should consider that a cage will likely interfere with the performance of the various side airbags. I'd think a little research would should that the rollover performance of the as-designed structure will easily suffice for a reasonable rollover. Comparing to a gen1 or gen2 is an apples to...
Fill up the radiator. It should be filled to the brim. Then fill the overflow tank to the cold line and drive for some days and see if the level in the overflow tank changes much.
Many dealerships have an express lube service for which you may not need an appointment. I've just used a drain pan that had a lid on it when in the same situation.