Hi Mash :-)
The main problem was that I bought an engine (off ebay) that had most of the ECU, etc but not a complete set of electronics.
If you really want to go down this route, my advice is to buy a complete car and remove all the loom, ECU, EWS, and a whole variety of other parts like the dashboard, clutch switches, sensors, etc.
I couldn't find anyone who would build an ECU with the security bypassed.
I'm sure it can be done, but....
Here is a sample of the description from the BMW training manual for their technicians
EWS III (3.3)
EWS III (3.3) is installed in the 1998 E38 from 5/97 production, in the 1998 E39 from 9/97
production, in the E46 beginning of production, in the E52 and E53 beginning of production.
Purpose of the System
The purpose of the EWS III (3.3) system is to add greater theft protection by providing a
higher level of sophistication than previous systems. The new “Rolling Code” provides an
additional theft deterrent through a changing of the ISN everytime the vehicle enters the
start sequence.
Components changed in the EWS III (3.3) system include:
• EWS III (3.3) Control Module.
• DME Control Module.
• Transmission Range Selection Input.
System Components
EWS III (3.3) Control Module
The EWS III (3.3) Control Module uses the same 13 pin connector as EWS III (3.2) but functions
differently. The EWS III (3.3) module has a “Rolling Code” ISN assigned to it during
manufacture. The “Rolling Code” is burned into
the module and cannot be overwritten by ZCS
Coding or DME alignment procedures.
The “Rolling Code” is a one way signal from the
EWS III (3.3) control module to the DME and is
similar in operation to the data exchange
between the EWS control module and the key
transponder.
The “Rolling Code” will be different each time the
start operation is begun. The “Codes” are taken
from the “Rolling Code Table” which is assigned
at the factory to the EWS III (3.3) control module
and the DME.
Workshop Hint:
While it is possible to initialize a key to another
vehicle to check for remote operation, use caution.
All keys for Both vehicles must be available.
The initializing process, causes loss of
operation of keys previously initialized.
All keys must be initialized at the same time.
DME Control Module
The DME Control Module has changed in that it is not the source of the ISN but now only
stores the “Rolling Code”. It compares the “Codes” to those sent to it by the EWS III (3.3)
control module. The “Rolling Code Table” assigned to the DME must match the table in the
EWS III (3.3) module. The “Rolling Code Table is “burned” into the DME during the programming
of the DME and cannot be change once “burned”.
Transmission Range Selection Input
With the introduction of the SKE type connectors on Transmission Control Modules the
direct input from the Transmission Range Selector Switch is eliminated. The input for range
selection is now received from the AGS Control Module.
On manual transmission vehicles clutch status is input directly into the DME.
Principle of Operation
The starting sequence of the EWS III (3.3) is as follows:
(Same as EWS III (3.2)
• The key is inserted into the lock cylinder and switched “ON”. The EWS III (3.3) control
module is powered through KL R and sends a 125kHz AM signal to the ring antenna.
The AM signal induces voltage in the key coil and powers up the transponder.
• Powered up, the key transponder sends the key identification code to the EWS III (3.3)
module. The EWS III (3.3) module verifies the key identification code and checks to see
if the key is enabled. If the key is correct and enabled, a password is sent to the
transponder over the 125kHz AM signal through the ring antenna.
• When the transponders accepts the password, it releases the changing code which it
received from the EWS III (3.3) module during the last start-up operation to the EWS III
(3.3) module via the ring antenna.
• The EWS III (3.3) module compares the changing code received from the transponder
with the code stored in its memory and if they match the process is allowed to continue.
The EWS III (3.3) module looks at the other inputs for correct status (e.g. Code function
not active, Transmission in P or N or clutch depressed, engine speed below specified
RPM) and energizes the the internal relay to begin starter operation.
New to EWS III (3.3)
• While energizing the internal starter relay, the EWS III (3.3) module calculates a stored
code from the “Rolling Code Table” and sends the calculated results to the DME.
• On receipt of the “Rolling Code” from the EWS III (3.3) the DME calculates it’s own
stored code and compares its results with the code it received from the EWS III (3.3).
If the “Codes” match the drive away protection is released and injection and ignition
are enabled and the engine starts.
If the “Codes” do NOT match, the DME “rolls forward” to the next code according
to the “Rolling Code Table” and makes the same calculations. The DME continues
this “forward roll” up to a maximum of 200 times or until a match is found. Failure
to find a match will result in the engine cranking but not starting.
• When the ignition is switched off and no engine RPM is present in both the DME and
the EWS III (3.3) control module each module will automatically “roll forward” to the next
predetermined code based on the “Rolling Code Table”. This new code is used for the
next starting sequence.
PM me if you want a complete copy of the training module, with diagrams...
Engine options for a Cabrio rebuild
I would also take a look here too: 
Linear Mode
