Note that I haven't tested all the possible permutations of member stuff yet (this was just a quick look around).
Since the db is probably not very large (if the forum hasn't been used much) phpMyAdmin should be able to handle any required operations without hitting timeout problems.
Suggestion:
Start by emptying the error log. It probably has a lot of accumulated crud, and you wont want to keep it.
Copy the db content to a new db, then point the forum at that. Mass delete away to your heart's content. Easiest way would be to browse the members table, order them by group (which will put the admins and mods at top) then export the rows for admins and mods only (just use the quick export, not the custom options).
Once you have the required rows exported, check the SQL file to make sure it has the content you want. If it does, drop the entire members table in one fell swoop. Then, simply import your SQL file back into the db. It will re-create the members table with only the content you want.
If forum then explodes, you know it didn't work well, and you can simply point the forum back to the original db. If forum doesn't explode, go into forum maintenance section of admin and run all the basic maintenance tasks. See what happens.
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