The amount of decking the head and block will receive is not enough to cause interference. If you are that worried about it then the easy solution is to get a thicker MLS gasket to compensate. But most of us never worry about it and don't have problems, at least for the first decking.
Grinding valve seats, and valves is factored into Toyota's design. This is why the factory service manual provides guidance on how to grind the valves and valve seats.
If you are taking the engine down for a major overhaul (200k+) and you don't grind the valve seats and valves you aren't fully...
Here are the possible leaks at this location:
Heater pipe gasket missing or damaged
By-Pass Pipe O-ring(s) missing or damaged
Water pump gasket missing or damaged
Water pump internal seal damaged, you'll see coolant pouring out of the hole on the bottom of the pump housing (replacement water...
Your oil gauge is useless, you need a true gauge showing true PSI. High pressure on a rebuild isn't atypical.
Also get a new version of your FSM here. I just organized the 93-94 FSM and made bookmarks to help navigate, you'll find the thermostat info in <2 mins