Going to replace the head gasket on my 89 Quadzilla tomorrow. Something I haven't done before.
I have new OEM studs, nuts, washers. an OEM head gasket and a repair manual.
Tips, tricks and knowledge you guys can share would be appreciated!

Easy so far but the biggest problem I have right now is removing the old gasket that is stuck to the head and cylinder. Certainly don't want to scrap this aluminum so what works best to clean the old stuck gasket remnant's off?

Use a sharp putty knife to scrape the big chunks off.  The gasket residue/adhesive is easily removed using a new flat whetstone with WD40 or some other thin lubricant.  The flat whetstone planes off the gasket remnants without removing or scaring the aluminum.

Last questions.
Which way do the small holes on the gasket go???
The manual shows that the small holes go to the exhaust. There is an EX on the OEM gasket but this is the OPPOSITE way the one I am taking off is. But that way does match up better on the top head holes......

So small holes to the front of the bike or small holes to the back of the bike?

small holes over the exhaust.

Yes. the small holes go above the exhaust port................. and one of the small sets of holes should be under the water outlet from the head.  The orientation of the gasket in the picture is correct. 

If the large hole in the gasket on the left front is placed on the right front, it can cause  the bridge between the left side exhaust port and the left transfer port to overheat and cause a piston seizure to occur in that area.

thanks guys the previous gasket was backards. No wonder i had issues with heat funny it made a week running in Glamis. Now i know why i was 10-15 degrees warmer than the other two zillas

The gasket being backwards WILL NOT affect the coolant temperature.  It could prevent the coolant from circulating over some surfaces in the water jacket making those areas of the cylinder wall overheat.  When an area on the cylinder wall overheats the oil will breakdown causing the piston to scuff and melt the surface of the piston skirt making a "seizure mark".

High coolant temperatures are caused by the radiator not getting rid of the heat to the atmosphere.  The radiator not getting rid of the heat could be any one or a combination of the following:

1.  The vehicle speed is too low, not enough air flow THROUGH the radiator.
2.  The small fins on the radiator are peened over from years of being blasted with mud and gravel, hindering air flow THROUGH the radiator.
3.  The radiator fins may have lint and mud preventing air flow THROUGH the radiator.
4.  The tubes inside the radiator may be partially plugged with corrosion.
5.   Air scoops are missing, bumpers, number plates or designer grills are preventing air from flowing though the radiator. 

If the radiator is working properly and the vehicle speed is high enough to get sufficient air through the radiator the coolant temperature will not be high, regardless of the way coolant flows through the engine.  The 250s and 500s were not designed to be run for more than about 30 seconds in 1st gear.  Anytime you spend more time than that, expect your coolant temperatures to soar to high levels.