Now that you have given yourself a base to work from, plug in and power up just like you normally would play with your Volume and Tone knobs adjusted on the guitar about half way but your amp settings where you normally would have them. Switch over to your neck pickup and start striking note's the way you normally play and from the distance you would normally position yourself away from your amp. It is important to do everything in a position you would normally play in. Focus your attention to the sound and tone coming out of your speaker or cab.
The following pickup heights are recommended by Greg Fryer on the Brian May Guitars website
Measuring at the centre of each Tri-sonic pickup up to the underneath of the string, set pickup height relative to each E string as follows:
(Measure with string at concert pitch and not fretted)
(It can be handy as a reference to fret both the Top E and Bottom E strings at the 24th fret and to measure the gap down to the pickup - this works fine with the Neck and Middle pickups but is less meaningful at the Bridge pickup)
Bear in mind that these measurements are to suit the original pickups on Brian May's Red Special and also the replica pickups that I have been recently making with Adrian Turner - these measurements might not suit the pickups on your guitar or those Tri-sonic's that have more powerful anisotropic ferrite magnets like the Korean made Burns Tri-sonic's and Kent Armstrong Tri-sonic's - so as usual the rule of thumb is: fine tune to suit what you think sounds best!