My suggestion/opinion for what it is worth and I deal with them every day is to build it the way you want. The car will take a big hit in value without the original drivetrain and if you put all numbers matching drivetrain back in it along with all the expensive engine peripherals you can expect to spend anywhere from $20k to $30k which you will never see. If you build it the way you want it then you will likely enjoy it more without effecting the value much. Again, just my opinion and I am a numbers guy.
Rick
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