Mick, this is a difficult question to answer as it is an exercise in compromises.
The placement of the engine should be defined by it's relationship to the diff pinion and this is compounded by the very short wheelbase of the cobra.
It is recommended there be at least 1° and a maximum of 3° angle on a universal in both planes and no more than 1° difference between both uni's. These limits guarantee a vibration free install.
Here are two sites illustrating the concept:
http://www.clubfte.com/users/jniolon...nephasing.html
and ...
http://www.drivetrain.com/driveline_angle_problem.html
The compromise comes about because our tail/drive shafts are roughly 300mm long between the trunnions of the universals so doesn't give us a lot of freedom with regards to engine placement. It is also compounded by the offset of the pinion to (usually) the right hand side of the car by some 30 - 40mm.
This whole exercise is worth doing to see what limits you have and what extent of shims can be used as mentioned by others to provide the clearance.
Once you identify the theoretical placement of the engine then you can make a decision about the sump. Maybe cutting and welding the sump to improve clearance and capacity is a better option.
see here for an example of an LS1 sump being modified.:
http://www.ls1.com.au/forum/showthre...t=cutting+sump
cheers