Knocking/tapping

My 89 supra n/a has been tapping/knocking at about 2k rpm and above for some time now. I replaced the rod and main bearings but still had the problem. I've just been babying her till I got up the money to replace the engine. Something weird has happened. I got tired of not going over 40mph (5th gear at 2k rpm). I didnt dog it out but had it up steady at 3k rpm for a while. Well, the next day it stopped knocking. It still hasn't started knocking again yet. It did have one spurt of knocks as I reved it to 3500 rpm but it stopped and hasn't done it again. Previous, I never noticed it knocking until I let off the gas, then I would hear a moderate aluminum sounding tap until it reved down to 1500 rpm or so then it would stop. Just to tell everything, the egr has been giving me problems(check engine light) and I noticed that the flange for mounting the egr to the manifold was broken and only held on by one bolt. Over time it also started to slowly progess lower to starting at 1700 rpm. 2DAYS later: it went away for a couple days but now its back and it moved, it now taps at 2500 and above. It is definately an aluminum knock. Would jumped timing cause this? Jumped a tooth or something? Computer not adjusting correctly? Knock sensor? I am totally at a loss. Any help would be appreciated