What would the difference in temps be if we measure from the glow plug and from the side of the block just below the cooling head?
Anybody has any input on this?

Thats not really a question that can be answered. Its all varied. Dependant on the motor , the tightness of the area it sits in , the kind of heatsink on it (again motor related). The exact spot you shoot it.

The best bet is to go for the glow-plug or have a temp gauge wired to one certain spot. This creates a more consistent reading , so instead of thinking its running hot one time and cool another just because someone might have pointed the temp gauge one mm to the left or right. Its always dead on.

Thats why I like temp gauges with lazer sights or temp guages that make you angle the head right into the top of the heatsink so its always pointing down. I forget which ones do this but just recently one was released that helps focus your aiming. Which makes it more consistent.

The rest is the ones that tie around your heatsink , this should provide a solid reading. Allthough extra weight. The only drawback is your readings will be more personal , rather than a shared reading with others over the internet as most people read at the glow-plug. So yours would be off slightly , but if you get familiar with yours motors and your temp guage then its effective cause you at least know the ranges you do and do not want to be in.

Beyond all that. I know some big tuners just use the spit or water drop test and they judge overheating by how quickly the water sizzles of the heatsink...

- Happy Tuning

go with the temp at the glow plug

I recently changed the head on my v-spec with a nova head and readings from the plug are way off.
I forgot to take measurements from the side and compare with the stock head...so i thought to ask here.
I tried changing the emisitivity on the meter but it doesn't seem to read consistently.

mainly you should tune by performance and not just by temps

What type or brand is the temp gun your using as for temping towards a tune that's just to get you in the ballpark.

I have an Ofna temp gun...
I do tune for performance...temps are only for reference.

I do not measure temperture when I tune my engines. I think it's okay as long as I can see enough smoke coming out from the pipe.