Ford focus not starting after engine change

Hi all,
I have replaced my 1.6 zetec se engine in my 2002 focus.
Unit has been replaced with another 1.6 zetec se but it will not start.
It cranks fine, sometimes sounds like it wants to start ( pitch of crank goes high as it coughs) but then returns to normal then battery goes flat.

I have done the following:

Re-timed engine
Checked plugs, I have spark and also tried with my coil pack from old engine
I have fuel spraying from injectors
Fuel pump primes
Key recognised on entry
Original wiring used
Swapped intake manifolds as new engine did not have MAP sensor on intake
Odd spray of easy start
Swapped crank and cam sensors from old engine
OBD showed- P0320 igniton speed failure (or something like that) told to try other crank sensor.

My old engine was hydrolocked in flooding, I have replaced clutch as my old one was noisey, new slave cylinder, timing belt pretty looks new ( couldn't replace due to pulley bolt) so I don't want to get rid of this car for pence when it must be something simple.
Any advice appreciated as I am well and truly stumped.
Thanks