Offroad-Express

Water in the diesel filter should trigger a dash light, but you can try draining from the bottom of the filter housing anyways. When was the diesel filter last changed?

If its the 3.0l 1KZTE.... there is a boost cut at approx 14psi...
Perhaps you are over boosting (just a spike)...now that you have opened up the exhaust a bit...When it comes in it feels like its dropped a cylinder...
Other than that..water.......injector playing up.....ecu on the way out....fuel pump on the way out

it would have to be going extremely lean to make it that noticeable.

i have an 80 series cruiser. 3 inch exhuast, front mount intercooler. stuck it on the dyno. at 10psi and at 14psi, 14psi makes no more power than 10, cause there isn't enough deisel going in to support more air. start spraying meths and water into, well thats another story all together