Alternative methods of setting the intonation on a guitar

[Mr Songwriter]

I like to think I've got a reasonably good ear for tuning, at least as far as knowing when a guitar is out of tune anyway, but I've often had trouble setting the intonation the conventional way - comparing the natural harmonics with the fretted notes at the 12th fret (possibly because the two notes are so close together or that it's quite easy to change the pitch by fretting the note just a little bit too hard) so I've been looking round for alternative methods for quite a while now, anyway I came up with this method:

 

(e.g. for the thin E string)

 

1) Tune the B string with a tuner and then tune the E string so that it sounds as 'in' as possible when you play a B5 chord with the open B and the E as follows:

 

E|--2---|

B|--0---|

 

2) Then go up the E string and repeat step 1 with the following intervals:

 

E|--4---5---7---9---11---12---14---|

B|--0---0---0---0---0-----0----0---|

 

...paying particular attention to the last one, if any of the intervals sound out then bend the fretted note up slightly to see if it sounds any more in tune, if it does, you will need to keep moving the bridge saddle backwards on the E string until the intervals sound correct.

 

3) Repeat steps 1 & 2 for the rest of the strings until all is well with the world.

 

..Does anyone else have any non-standard methods for setting intonation? and are there any problems with the method I'm using here?