It's fine to have a secondary drive as it's own -- no need to slave. Question is, was it a slave before or just another drive; either way is fine but it would affect the jumpers. I strongly suspect your jumpers are fine so I wouldn't mess with them. Losing one in the carpet is a bear!

The connection you unplugged sounds like the power cable, so as long as the connector fits, it wouldn't matter which one you used. I am drawing a total blank on Win 98 right now -- I managed to mostly skip that OS. I know what I would TRY first, but it's the kind of thing I wouldn't want to tell a novice to try; too risky. Maybe JohninKansas will log on tonight. He seems to know or dig up quickly the obscure stuff.