Heres my two cents, take it any way you want. You say it runs smooth, which rules out a bad, bent, broken, or otherwise faulty pushrod. If it was a bad, bent, broken, or otherwise shitty pushrod, trust me, it would not run smooth. Do yourself a favor, dont guess at any of this, check these things out. Flexplate bolts, maybe.....if you are suspicious then slide under there and check them, its easy.
The only way to check for a cracked piston skirt is to drop the oil pan. I had this issue for a LONG time. The noise started at about 60K miles. The noise, clacking that made it sound like a diesel engine, got a little louder over the years but eventually stabilized. I finally dropped the pan at around 210K and immediately saw the missing skirt. The chunks were in the pan. I racked up all those miles, on road and off road, with that damn clacking noise and it never came apart. It did the same as you are describing, 'went away' at 2000rpm. I continued to drive the damn thing until 219K miles, when I shut it down for good to rebuild the engine. The engine factory used cheap crap parts in the engines, but it still ran a long time. So my advice is, if you can at least afford to drop the oil pan to check the skirts, do that. If it is the skirts and you cant afford the rebuild right away, so what, just run the damn thing. At least you know what the issue is and you wont be constantly trying to figure it out. You dont have to beat the hell out of it, although I never held back with mine and occasionally hit 4000rpm and that piston (#6) never came apart, but will probably be ok for quite a while until you are ready to rebuild it, which doesnt cost all that much either! Good luck man, any questions just ask. Good Luck!