You could make a test for finding out, which pairs have priority. You can limit the maximum number of pairs to less than 2048, 100 pairs for example. Then you build class kerning, that results in 110 expanded kerning pairs. 100 of them are combinations of letters. And ten are combinations of letters and point, comma et cetera.
Additionally you could create your own codepage, which you select in the font window and in the drop down menu "generate only pairs with glyphs in following codepage".
I assume, that those pairs with the most extreme values have priority; this would make sense.
I did not check, if it works, but in this way you could create your own codepage:
1. Remove all characters from your font, that shall not be in your codepage. Every character should have an Unicode value, even if it is a value that belongs to the private use area.
2. Generate the font.
3. Decompile the cmap-table with TTX.
4. Open the decompiled cmap-table in a powerfull text editor like UltraEdit. (A file with character names and Unicode values.)
5. Search and replace with regular expressions and create a syntax like this one:
%%FONTLAB CODEPAGE: 0xFFFF; Ray
0x41 0x0041 % LATIN CAPITAL LETTER A
0x42 0x0042 % LATIN CAPITAL LETTER B
0x43 0x0043 % LATIN CAPITAL LETTER C
0x2D 0x002D %HYPHEN-MINUS
0x2E 0x002E %FULL STOP
0x2F 0x002F %SOLIDUS
0x30 0x0030 %DIGIT ZERO
0x31 0x0031 %DIGIT ONE
0x32 0x0032 %DIGIT TWO
0x33 0x0033 %DIGIT THREE
6. Save the file with the extension ".cpg" in the FontLab folder, in which the codepages are stored. On Windows this is "FontLab-installation-folder\codepage".
7. (End and) restart FontLab.
If you want to change the unicode later, that should not be a problem. TTX also can decompile the kern-table. And the kern-table can merged into a font with different unicode values. You must not change the character names only.
I strongly recommend TTX. With the help of batch files it is very easy to use. Alternatively you may give OTMaster a try, but I think, that the prices of DTL products are elitary and I like free open source products, projects, which everyone is allowed to improve. I am for my part very contented with TTX.