Power issues can cause massive hard drive lag. I don't know if SMART would catch that. Just a thought.
The power supply itself can be an issue, but also molex connections that have been plugged in and out a number of times will loosen up so that the metal parts in the plug won't make good contact -very common issue, but generally associated with system freezes as well as lag.
We had a computer here that was really bad. It would take like twenty minutes for the hard drive light to settle down when loading winblows. You couldn't do anything for that long, and it was like any button you hit caused the hard drive light to come on full load for minutes and the system wouldn't respond. It was that way for years. Somebody over here just to like complain I think. But it finally broke for good after I did a hard reset on it on one day when I was in a hurry. I hardly ever used that computer, almost never, and there it broke on me. It had been to the shop previously and the smoozer over there didn't even bother to upgrade the 1 GB of RAM, but he did come over and sit on his ass and chatter with not me for well over an hour. I was told it was just so much better after that. Not. Wrong. Nonsense. Turned out to be a power supply issue. It was one of those really, really cheap power supplies. I opened the box to disconnect the hard drive before evaluating the hardware. Couldn't get the optical drive to load a liveCD, really weird activity. Swapped it with a quality power supply and that did it.
Be real, be sober.