You want to have the probe between 3 and 6 inches from the valve for your best readings. A bung would be a good idea on a tubular manifold as well.

Also, nearly all shared plenum hondas have an air bias problem on cylinder 3, NA or forced, so that would be the best cylinder to monitor if you can't monitor them all.

For the record, I've used EGT's racing 2 strokes [which are far more sensitive to improper A/F ratios than even the most high strung turbo engine] for the better part of a decade.