Any suggestions on a good tap and die set that covers the FJ40?
Cheers

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True. I have the whole set, and use different taps on different cars. On the Toyota, most of what I'm cleaning up is M6x1.00, M8x1.25 and M10x1.25. Those three taps will take care of 98%.you only need 3 or 4 taps.
I've been using a 39-piece Craftsman set (9-52383) for decades, on all manner of Japanese, German and Italian vehicles. Haven't found anything on the 40 that it doesn't cover. No idea if they still offer a similar set.
I know that it does not make common sense, but you want 'high speed steel,' not 'high carbon steel.' This was what we only used in the machine shop for even hand tools. But even at that, don't expect them to last long cutting thru rust and welds. Three-fluted types are better than two-fluted for recovery work, and be sure to not cross-thread by being perfectly perpendicular. And, you will also need a tap handle for your tap and EZ Out screw extractor set.
If a captive nut is toast in your body or whatever, you probably are best drilling them out and using a Heli-Coil insert. When we used to do areospace jobs, they actually specified them for every internal thread that was not a pipe fitting.
Replace the fastener, because a die cuts a sharp corner and critical fasteners were very likely rolled because it creates a totally different part in a metallurgical sense. It certainly does not hurt cleaning up a male thread with a stiff wire brush.