I say you need to look at things physically as you are doing, but with more logic being used.
To me the only place something can be off from the last time everything was bolted up would be where the motor mounts bolt to the block.
This is the 100% only location where since the mounts bolt up perpendicular to the ground, a up and down change in the installed height to the block will not change the V dimension like anything else will if something is not right!
In other words if your new frame mount are made wrong or bolted to the frame off position that can make the V taller or shorter, and either way stuff will not bolt up right.
I hope I am explaining my thoughts clearly?
PS.
You need to be careful because if it is the engine sitting lower then your fan may be only 1/2” away from hitting the bottom of the fan shroud.
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I do stuff for reasons.
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