For that frame rail part I can give you my interpretation of why some remove it. I think almost everyone has removed it. I have not. When it is removed and you make a new plate, you are able to mount the front of the sub frame up higher in the car. This according to what I read online about custom drive shafts for 4x4 and hot rod projects is better because there is less of an angle between the input for the differential and the tail stock of the transfer case. From what I remember seeing, everyone that has gone this route has had to modify the rear part of the exhaust tunnel because the drive shaft is up too high and causes clearance issues.
I went a different way. I did not remove those pieces. This did not cause a problem with my exhaust/drive shaft tunnel while I was using stock parts. It did make the drive shaft come close to the stock rear sway bar. About a 1/4'' clearance. Here is a pic of 1/2'' tubing on top of the drive shaft.
While I was building it, I thought the drive shaft would be coming really close to the front cross over piece, so I lifted the center section. This was not needed.
I replaced the stock dsm sway bar with a bigger unit since then, and it still did not cause a problem with clearances.
I only came into problems with the exhaust/drive shaft tunnel when I changed the drive shaft from a dual piece to a single piece
. I then had to raise the rear most part of the tunnel, I think it would have to be raised more if I removed those frame rail pieces. I do not suggest going with a single piece. Its great and everything because there is no bearing to worry about mounting, leaves more room for the exhaust and less u-joints. It works fine driving normally or even accelerating hard, but when I leave the car in gear at upper engine rpms there is enough engine braking that the drive shaft starts to vibrate horrendously. Once I push the clutch in the vibs are gone. I since found a drive shaft bearing that I am going to order up that should fit better than the stock dsm unit and change back to a two piece shaft.
Those are my ideas.
What is easier than one tow hook spot to the other tow hook spot for the front motor mount?
I do plan on changing a few mounts and stuff on the car over the next year. Hopefully for the better.