If you are using a non-standard battery for the Focus that may be the reason. Fit the battery type & capacity as recommended for the Focus 1.8 TDCi and ensure the various wiring connections go back on to the terminals in exactly the same order they were removed.
Also after refitting a battery the engine will need to be run for a few minutes to allow the PCM to relearn things, and the electric windows may need to be switched up/down to reinitialise them, also check other electrical items function ok.
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