I bought a 5.9L that had a small amount of front end damage. It has a NY salvage title. I know the procedure is to document VIN's and reciepts of parts used in the rebuild. I didnt know how pickey they are about the documentation. Like could I get parts off someone locally for free and not show a receipt? Also how do they know what to look for in the inspection? Is every damaged part accounted for when they issue a salvage title?

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First off have a receipt for EVERY part that you replace on that vehicle. If you buy used parts then get valid receipts for that also. If you buy a donor vehicle make sure you bring along a title that is in your name not just an assigned title, along with the bill of sale. I took many photos of the donor vehicle I bought so they could see why it was used. Document every step of the rebuild with photos. These troopers are the best at spotting any alterations trust me. I do not think they will pass a vehicle that is modified at all. If the vehicle was a six cylinder automatic it better be a six autoimatic. I did drive the vehicle to the inspection station in Bridgewater MA using a set of dealer plates owned by the guy who painted it. He came with me for the inspection. What they are looking for are stolen parts and that all emmission/safety equiupment is in place. Needless to say the quality of work done is important also. If you have a receipt for every last bulb, switch etc along with pictures showing every major step in the rebuild you should be alright. I brought with me about a two inch thick pile of receipts for items bought indexed to reflect the rebuld process, and about a hundred pictures in an album format. They checked EVERY receipt and then a punched them wth their receipt tool and went throught the whole album during the inspection adn asked questions of a technical nature given that I did all the mechanicals and my body guy was with me. They actually commended me on doing such a nice job.
The guy who did the body/paint gave me those basic guidlines since he dhad doine many rebiulds over the years. By the way they don't play games. They are as tough on you the hunderth time you have been there as they are the first time, but it is doable if you are thorough and meticulous with your documentation/work.