When I was having CPS issues it did almost exactly what you describe. Is it possible a connector or the wiring is fubared between the CPS connector and the ECU? I know from experience it is easy to clamp a wire when putting a motor in.
Is it possible the CPS bolts are loose or the CPS got banged during installation, improper pickup distance from the tone ring can also cause the same issues.
When you set up TDC, did you use a compression gage to make sure you were on the compression stroke? Don't assume, do it again, as many times as I've set up TDC I still screw it up on occasion.
Have you done a compression test on the new motor yet?
As a last resort, set up TDC, turn the motor over a few times and set up TDC again, I'm thinking the drive gear for the distributor may have a broken pin.
Most likely to be the CPS, the distributor, ignition, timing related or valves. Though anything that really screws with the mixture may be causing grief. Way too lean or way too rich can make it pop and buck.
Initial timing, turn the motor over until the compression gage registers, align the timing mark to zero. Curve a piece of coat hanger and stick it down the spark plug hole (bend/curve out, towards the valve cover). Back the motor by the harmonic balancer bolt about a quarter of a turn and then turn it to the right until the timing marks align, then go past the timing Zero. What you are trying to do is feel if the piston is all the way up when the timing mark is aligned to zero. Your last movement when aligning the timing mark should be to the right, this takes the play out of the timing chain. If the harmonic balancer bolt unscrews on you, you may have to remove the inspecting plate and turn the motor over at the tone ring starter gears with a screw driver.
An alternate methode, is to put the number one piston top of the compression stroke, timing marks aligned to Zero and then wiggle the intake and exhaust rockers, they should be a little loose and wiggle some. Pulling the valve cover is a pain, but this will sure tell you for sure you have TDC and what kind of shape your timing chain is in.