ive highlighted before that ive fitted GSXR600 throttle bodies to a 2 litre zetec and had it running on the orignal ford sensors and 2litre ford (DEWY) ECU. Its always seems to been running ok but today had it on a Rolling Road to check the fueling and power.

as can see from the graphs Red line is with the individual throttle bodies, Blue line is an overlay of previous run with the orignal inlet manifold and throttle body.

as you can see its current lost torque but breaths better at the top end with a healthy 148bhp @ 6250rpm from standard engine with tubular manifold and cone filter.
Also talking to the RR operator thinks drop in torque may be ignition map, which may be down to me using the GSXR TPS which has a max 3.8ohm resistance compared to 4.2ohm of the ford item so at full throtle ECU only on the 90% throttle map never 100%.
Reason for posting is problem people have with space with orignal inlet manifold, its on my tin top but may be a idea for others.

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Interesting always wondered if this would work.
Have you thought that perhaps the MAF is not helping either?
Have you had the ecu mapped? I'm sure if its an eec-v it can be done to a degree might help a little