I recentley swapped my engine for the exact same engine but when i fitted it it wouldn start it something to do wit a immobiliser on de lucas diesel pump on my peugeot 306 TD
you should have swapped diesel pumps over this is where your immobilizer is. if you have a chip in your key, you could get chip out of old key and swap it with yours. or you will need to code it the same as the pump if you have 4 digit code from old car, using a diagnostic machine at garage. or swap diesel pumps.
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