How badly does the engine run? does it idle like when you first got it? have you tried compression check on all cylinders? it could be somethings possibly relating to rings, balencer, crank, rod, basically bottom-end engine... but i dont understand the part of the 2nd gear, what that has to do with it. if it was in the
tranny, id say planetary gears, or valve bodies, but you say youve replaced the
tranny. How much HP are you pushing? you might have twisted your driveshaft or U-joints. Centrifigal parts have a weird way of acting up when they want to. One way to see if you can make it is jack up the rear end and try and get it up to that speed and have someone see if they can hear or see the noise... it might even be in the axles. OK, enuff ranting by me tonight, im gonna get another beer.
Let me know
~*Adam C*~