5BA is 43.1 tpi, so 14 thread pitches of 5BA is the same length (more or less) as 13 pitches of 5-40. This means that after 7 pitches, the crest of one thread will meet up with the crest of the other. %BA is also bigger OD (only by 1 thou). Putting 5BA bolts in 5-40 holes doesn't sound at all right to me. You can't get 1/8 * 40 nuts and bolts, so you'd have to make them, in which case you might as well make 5-40.
You can buy 5-40 nuts on e-bay, but the postage from US is silly. What you need is a relative over there to buy them for you and then send them across. A more radical solution is to drill them all out and fit M3 helicoils, but that might be a bit OTT