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Not that the PNP couldn't cause your car to start but I have never seen one do it. Usually you will just get the flashing yellow arrow and have a code stored for a bad gear position sensor. If you took the battery out and ratcheted the gear selector through it's positions a few times and now it does not start I would have to be more suspect of something you inadvertently screwed up while you were in there. Possibly you failed to reconnect something or knocked something loosed and did not even know it at the time.
The thing you have to do with the "R" is make sure that the reverse lights come on. To adjust you rotate the switch. If you look at the switch you will see it has two mount holes, one is a simple round hole and the other is elongated and allows you to move the switch around a little bit. You need to have it in place and ready to be tightened down and then put it in R with the key on and see if your reverse lights are on. If they are not on the go ahead and move the switch a little bit until they are on. Then check to see that the starter will engage in P and N. When you have all three, you are done. I have even gone so far as to have someone hold the key in the crank position while I moved the sensor around, when I find the sweet spot they let off of the key and I tighten it down and check for reverse lights.
Yes, you will need to have the battery in to perform these steps and yes I have no doubt it will be a little awkward but it should be doable. Myself, I use the tool on the 850's and use the method I have described to you above on the 960's as the tool only works so well on them and they lend themselves to the above method a little better than the 850's do.
Take a look at the Bay 13 tutorial on changing it out and if you think it is more than you want to tackle then tow it to someone who will. That tutorial does not appear to address putting it back together without the alignment tool. You can do it without it as I have described but it may be a little tough if you have never done one and are not entirely sure of what end results you are trying to achieve.
Good Luck, Mark
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