So here's a guide I wrote to help people having issues.
Check your head with a straightedge and feelers for warpage. Also look for any scratches.
Resurface the head with 600 grit wet and dry sand paper and WD40 on a flat piece of glass IF it is out of spec. Resurface in a figure of '8' motion, rotating the piece 90 degrees every now and then for an even surface. You will need to remove the centre intake valve as it sits slightly below the deck surface. It is also a good idea to briefly resurface the top of the cylinder.
Trial fit the gasket to make sure that the bolt holes and dowels/coolant dowels all line up. The gasket must sit flat, if it bows a little because the holes aren't spot on, you can carefully modify the dowel/bolt holes in the gasket with a dremel. Mismatched dowel holes will apply hundreds of pounds of nasty horizontal force once the head is torqued down. It's a recipe for failure.
Use brake cleaner (best solvent ever) to THOROUGHLY clean the gasket, cylinder and head surface, it MUST be squeaky, squeaky clean, no finger prints, no oil, no nothing. Also don't bother with gasket compounds, they tend to be a common solution for people that don't install gaskets correctly. These metal head gaskets are designed not to be used with other compounds.
Carefully fit the cylinder and head without touching or getting oil on any gasket surfaces. Drop the head bolts into their bolt holes.
Place a socket on the head bolts and finger tighten so the head is sitting level, then torque the head down in small increments of 5 ft lb's til you get to 27ft lb (from memory thats what YZ/WR250F head bolts are torqued to).
Every time you tighten a bolt, it loosens the next closest bolts, so if you torque each head bolt once, you will end up with loose ones.
So for each 5 ft lb graduation, keep torquing in a criss cross pattern until all the bolts are equal tension, then adjust your wrench another 5 ft lb and repeat. This endures your whole head is evenly torqued down.
Once it is all together, run the engine for say 3 heat cycles (heat up, cool down) with PLAIN WATER only, no coolant, to let the head gasket bed in or 'settle'.
Chemicals in coolant are actually slightly harmful to new gaskets. Once you have heat cycled it, drain the water out and put your favourite coolant in. Never leave plain water in the cooling system for more than a day, it will corrode aluminium and rust steel, and it is prone to freezing which WILL crack your head and possibly cylinder, believe me I had this happen once and it was not fun .
I hope this helps you guys out.
Additional info from TT members:
Also, not manufacturers torque spec, manuals are not always accurate. Think about the bolts. If you know you have everything right and still have gasket failure (not due to a massive overbore and resulting minimal wall thickness) the torque specs may be too low.
Finally, be sure the threads are perfect on the bolt and case. If the torque specs specify oiled threads, use oil, not anti-seize. If dry, make the treads truly dry. Torque in small steps, in a crosswise pattern. Use a good wrench.