micka, the flywheel normally rotates clockwise when viewed from above, so the firing mark has to be clockwise on the flywheel from the TDC mark for it to fire before TDC. So far as firing is concerned, the GV400 owner manual says:
"Adjust contact breaker points so that they just start to open when F mark on flywheel aligns with the mark on cylinder barrel." It also says:
"IGNITION TIMING: 20 degrees BTDC (fixed). The CDI type does not require adjustment."
So, does your engine have breaker points? If it does, they are in the center of the flywheel, together with the coil. Whether it has points or CDI, I cannot see any way the TDC mark could be wrong unless the flywheel key or keyway is damaged. Incorrect camshaft timing cannot cause the flywheel timing mark to be wrong. I think you need to pull the flywheel and have a close look at the key and keyway. When you have them in good condition so the TDC mark is correct, you need to adjust the points in line with the instructions above, so it fires at the F mark. (I can't understand how they can have it fire at 20 degrees BTDC without kickback, but apparently they somehow have that taken care of.)
For tappet clearance the owner manual says:
"Measure at TDC on compression when engine is cold."
I think this is what you did in the first place, before I confused you with information from the small GV engine's manual, which turns out to be quite different for the GV400. So, it sounds as if your tappet clearances are now OK, following you grinding the stem of the inlet valve.
So, a lot of the confusion up to now has been due to me reading the wrong manual. The GV400 manual does not seem to be available on this site, but you can download it free, from here:
http://engines.honda.com/pdf/manuals/3189120.pdf
