Whats the best way to do the valves on a 3tj?

Take the engine out and do it on the bench

Measure all clearances

Turn to TDC, mark the timing on the chain to make reassembly easier (dot of tippex) remove camchain tensioner then take out cams (inlet cam needs dowels removing to get clearance to get the cam out and it is done with the sprockets still attached) & all buckets & shims (magnet on a stick gets bucket & shim out easily).

Lay everything out on a clean surface in the right order. I use a length of paper off a roll of lining wallpaper, so that I can write all my clearances & shim sizes before and after etc. on them.

Swap shims & get new shims, etc. to get as close to maximum clearance as possible. If you're not within 0.03mm of maximum then I would change the shim because clearances always close up and the reshimming takes much longer compared to swapping out an extra few shims.

Reassemble including tensioner & double check timing. When the shims go in, make sure they are seated properly (they should spin easily using your finger). Put a dot of MoS grease on the valve top and then agaon on the shim once it's in.

Turn the crank a few times to settle everything and then recheck clearances

Nice one Plodder, Would you think 0.05mm clearance on the inlets would cause problems? and is setting the clearances to near max for any performance gains or to just save doing them again soon?

Closed inlets like that cause starting problems.

I think the YZF750 SP racing manual says to go ~0.03mm over spec, so there may be some performance advantage but as the clearances always close with time, setting everything to max gives you the best return for your time because if you consider that it takes 5 minutes per valve to measure, calculate, change shims and re-measure, while it takes 3-4 hours to take the engine in an out, then I don't see the point in not making them as good as they can be.