Okay so posting in this thread after having more experience with the game. Here's what's what for those not in the know. In the Tuning Shop under the extreme tab you can install a new body which will remove all installed weight reduction parts, however despite its name a new body will not undo the widebody modification. And because of this, there is currently as of 5/23/22 no way to undo the widebody modification.
For engine upgrades, such as bore up which are permanent, under the extreme tab you can buy a new engine which will restore the engine performance to the factory performance of the engine you have installed. If you have say an engine swap installed the new engine feature will keep that engine installed and will not give you an option at all to restore the original factory engine that comes with the car. In short you are stuck with the swapped engine.
Wings, and other visual tuning parts excluding the widebody, are all able to be undone/removed in GT Auto.