my car does this sometimes also but it's not going from D to OD.
are you running an aftermarket coil or ignition parts? if so check the cap and rotor. last year i was having ignition problems, alot of burnt wires from the headers but that was obvious. the in obvious part was the cap and rotor burnt up in 3 months. Car runs hard in 1st and 2nd but top of 2nd and going to 3rd falls off and catches again. went with the Accel cap and rotor to match the supercoil and problem fixed.
when you did your headers did you put a heated O2 sensor in? this will make it go super rich and going into third does the same thing i just mentioned but not as noticable. i put my heated O2 in and found about 30 rwhp after the old one fouled out. it doesn't take long for it to foul. put a 5 amp fuse in (as recommended by some forum members on CF) and it popped it. i knew it and had 2 races lined up the next night. sand bagged on a bad tune. next day popped the hood to check the fuse and it was blown. put the stock 30 amp fuse that came with the fuse block and back to blowing the tires off in 1st gear at a 30 roll
if your tune is off what happens is the car is not geared through the rear or tranny to compensate for a lack of power and will bog until it has enough RPM to pull through it. our cars with 2.59 rear gears and a 700R4 tranny isn't the perfect match but it works. the low 1st gear of 3.08 (i think that is what it is in a 700R4 i know it's 3. something) means something has to give in the other gears. 2nd is stretched alittle and third is stretched alot. so this means with every gear shift the car is pulling less and less and when the tune goes out you really notice it in 3rd until the rpm's are above 3500 rpm
It's all about the Tune.....