There are 1156 pairs in the file, but most of those glyphs do not exist in your font, so only 95 new pairs are produced with a total of 117. Since you already had 47, then only 70 of those 117 are completely new pairs, the remaining 25 are new values for the existing pairs, and 22 pairs will retain their old values because the difference is less than 25%. To avoid replacing old pairs, increase that 25% value to 1000%.
Thanks, that explanation makes sense. I did that and it worked…though after running a few more tests I think somehow the first time I did it I must not have selected the option to include existing pairs like I thought, because trying it both ways I discovered that it only overwrites my manually set kerning if I don’t include the existing kerning pairs.
As it says in the other thread, not all applications do support kerning. Lowercase at least should work without kerning.
Well, I’ve designed my font so that the lowercase are identical to the uppercase, except for the ‘I’ (it’s a comic book thing)…and after some more testing I discovered some interesting things. First, Illustrator does support kerning…but I was getting confused because pairs like ‘TO’ were showing up with large gaps despite me having tightened them up already. What I missed was that the two kerning pairs I’d created were both using the capital ‘T’ –meaning I’d still need to go back and make two more pairs to include the lower case ‘t’ (which in this font appears identical).
Is there by any chance a way to automatically duplicate the kerning from the caps to the lower-case characters 
The setting also depends on the font size. Usually word-processors will enable kerning only above a certain point size.
I noticed the concern over font size and that the setting can be modified, and it still didn’t appear to work at any size when I tested it on Friday…but I think that was because of two factors—first, because of the problem I mentioned above with pairs like ‘TO’, and because last time I just typed random sentences, not the whole alphabet from ‘A-Z’…so I didn’t really see my manual kerning in action. Today I did both, which was part of how I discovered the ‘TO’ blind-spot I was encountering.
First design the glyphs, then manually adjust the side-bearings using the Preview Toolbar and/or glyph comparison toolbar. Autometrics is just a quick and dirty method. There is no way that a font needs the same side-bearings on A or W as it does on i, j, or y. Look at some existing fonts that are similar to yours, and see how they compare…and see how many kerning pairs these fonts have. You can export a list of pairs from one font as a text file and use it for other fonts.
I opened a number of fonts, and none of them had any kerning pairs, which I found to be interesting. I looked at their metrics and saw that they varied in width from character to character…but each font was different in this regard. I can see now that modifying the metrics before moving on to kerning will reduce the number of potential kerning pairs…but what I don’t have a sense of is the type of methodology or pattern to doing this correctly. You mention that it is known that certain characters need more or less than others, but how is that determined 
Is there a rule of thumb to follow, and if so, what is it 
I see that by using the comparison window I may preview how each character rests next to the others…but I feel like I’m missing the bigger, intuitive picture of how to wisely use this tool when adjusting the metrics for a given character to minimize the need for kerning, later. At this point about the best I can do is screw around and try things, but I get the sense that there are some basic, tried and true techniques you pro’s are using that are not plainly stated anywhere in the documentation that a newb like me would find immensely useful.
Part of my problem may also stem from using all caps (except for I), introducing a component I’m too naïve yet to fully appreciate. Any ideas on that 
So, if you’re relying on kerning to make your font look good, it will only look good in applications that do support kerning if users enable it. As far as possible, design your font not to need it.
What I’ve noticed is that if a font is designed so that the outlines of the characters adhere to a regular rectangular shape then when the characters are lined up end-to-end they are going to look mostly ok, and the standard kerning would probably handle most of the needs for such fonts. The bold version I designed isn’t as rectangularly uniform, which is part of my conflict…and I’m thinking at this point—though I’m not certain—that by skewing it I’ve exacerbated the apparent distance between certain character pairs.
Since there does not appear to be an a-z tutorial on font making either in the manual or in the forum and it’s things like this that are not immediately intuitive, if you or anyone else can share some insider tips on how to intelligently and wisely adjust the metrics to make a font look as good as possible prior to kerning I would appreciate it immensely.
Thank you for all your help thus far!