Ok, so not exactly understanding what would happen I got my brain back but I hadn't done a bunch of quests yet and now it appears that my only avenue to to speak to Kline (SP?) and that starts a fight no matter what you say to him. I had another quest going where I had just talked to "O" and he told me to speak to Kine about other people wandering around the big empty so he won't talk to me about it now. You actually can't put at least the brain back once you get it to my understanding (I tried) though so I'm not sure what your meaning is regarding having the option of "switching them out again". Can you expound on that a bit? I saw this thread and it's remotely where I am at so I hope I'm ok posting here. I sure wish that I had saved just before taking my brain back though becasue right now it appears that my only option would be to start all over again in the big empty by deleting and downloading OWB all over again to be able to play through all of the quests that I want to. If anyone has another work around having to do that please tell me.
Once you complete the main quest, you can use the Auto-Doc to switch in/out your brain, heart, and spine. At any time. You need to complete the main quest though.
You furthermore don't have to fight Klein and the rest of the Think Tank. A fight can be avoided by passing a speech check, medicine check, or science check. Alternatively, if you've done the side-quests for the other Think Tank scientists (which it appears you haven't done), you can avoid the fight by getting Klein to confer with his colleagues. They should then take your side and you can avoid the fight without passing the checks.