The fix is to connect the prototype and set up the tests on the terminal, but also make sure you have the regular model available, because that's the one he'll end up using after you use the prototype to set up the tests. NOW - I had already built the regular version by this point, so Clem wouldn't use the prototype. Once successful (you'll know because you won't get an error), close the console and look around, and it should have spawned the prototype next to or behind you. This will save you from having to type a bunch of long lines. FYI: To repeat a console command or to edit one you just used, open the console and just push the 'up' arrow key. If 05 doesn't work, try 00, 01, 02, up to 09 until you find one that does work. So, when you begin the quest, but you don't have the prototype in your 'special' menu because you did scrapall - simply open the console and type (without the quotes, and capitalization should not matter) 'player.PlaceAtMe xx004bf9' - the 'xx' prefix should be replaced with '05' - at least, in my case, then press enter.
However, most people would have no way of knowing that ahead of time, so if you already did that and are stuck and don't want to reload an older save, this is how to fix it.
It's best to wait until after the Vault 88 quests before using the scrapall command.
