After upgrading my HD, my Mac stalls a lot

A while ago, I replaced the HD in my mac with a Hitachi 7200rpm 500MB disk. This was to replace the 250MB disk which had failed. The problem was diagnosed here Do I have to replace my logic board

Ever since, 2 things have happened. The life of the battery has shrunk quite dramatically, and the mac stalls quite often, with the coloured spinning wheel appearing from anything between 10 seconds to a minute or so. Sometimes it doesn't happen for days, and sometimes it happens 10 times in the space of a few minutes. I thought perhaps it was Safari, but it happens in other apps as well. I would be greatful for any help. It's quite puzzling. All advice I have had so far is that it must be to do with apps. But it appears this is not so. In the above diagnosis (link), a faulty disk was also excluded. (I have reformatted the disk using "write zero option" and I have done the hardware test, which reported no problems.