Craig, Congratulations on the performance of your motor. On the vibration issue, did you check the angle of of the front and rear ujoints ? They should be close to equal . If they are not it causes the driveshaft to speed up and slow down with each revolution and can cause a bad vibration. May need to change the height of the back of the trans. to get angles equal. Good Luck, Mike

Craig, Congratulations on the performance of your motor. On the vibration issue, did you check the angle of of the front and rear ujoints ? They should be close to equal . If they are not it causes the driveshaft to speed up and slow down with each revolution and can cause a bad vibration. May need to change the height of the back of the trans. to get angles equal. Good Luck, Mike

Might try taking the run out on the diff yoke.
Could have got a bad one. Assuming that is the only yoke you haven't swapped.
Also there are shops that can check the shaft while it's on the car. Might be a long ways from where you live though.
But they can narrow it down real fast. Read an article on a guy who jumped through all sorts of hoops just like you are.
Went to a shop that could do it installed and fixed it quick.
I do recall he got a new shaft that had excessive run out out of the box. Might check that just to be sure.

His problem turned out to be a minor diff in the T400 yoke ID.

As far as motor mods- Brodix 18X heads

I threw on two other driveshafts today. One was like a 2" v6 shaft, and it reduced vibrations. I put a 3" aluminum stock LS1 unit on there, and it reduced vibrations significantly.

So, looks like it's the driveshaft. The differential angle at the rear is about 3-4 degrees (nose of pinion down, shaft going up to tranny). Angle at tranny joint is almost zero, and no real way to adjust it. I'd like to raise the rear of the tranny to make the angle at the front about 2 degrees (angling down from the tranny to the shaft) and then have it angling up in the back the opposite way (up from the shaft to the pinion).

Anyways, I think the 3/5" steel shaft I had made is the culprit. It's just a hair shorter than it probably ought to be, and the engagement into the tailshaft might be a little less than desired. But I don't know if this is the cause.

Bottom line, swapped the shaft and it cleared up pretty much (like 95%).

Now back to the EFI -vs- Carb aspect. It's getting pretty cold around here now (like in the 40s, cold for here!). This motor just fires right up when cold, and idles like a big-a$$ed kitten purring. Rock-solid and smooth. If my FPR didn't bleed down or it was on a constant-on circuit, it'd be even better. Try that with a Carb?

Removing downward pinion angle = loss of traction.
A carb with a computer can idle just as smooth. It is not the FI that makes it idle well. It is the E.
Good to hear you have the vibration fixed.

How about MPG differences? hehehe. Just curious ...