Nevermind, I got it. You can add custom classes to individual inputs with the attrs column in the attrs column of the sys_form_inputs table with a serialized associative array.

For example:

UPDATE `sys_form_inputs` SET `attrs` = 'a:1:{s:5:\"class\";s:10:\"ben_did_it\";}' WHERE `sys_form_inputs`.`id` = 3

Then, just add the SQL code to install.sql and uninstall.sql for your module. Thanks for your help @LeonidS.

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