The AJ6 came in both 3.6L and 4.0L versions, and although the 4.0L had
more torque it really did not make more power than the 3.6L.
Over the years as emission standards became stricker, it became obvious
that this engine needed more computing power and gadgetry to reverse
what was happening to this engine; it was losing power whilst
competition was making more and more power.
Along comes the AJ16
The block casting was lightened yet made more rigid and allowed the
designers to place mounting ears for knock sensors right where they
would work best. It boasted a new fuel injection system and a throttle
valve with the idle control built right in. The head was revamped and
received new valves and castings to mount individual ignition coils
over the spark plugs. Newer piston design raised the compression to
over 10:1 and a higher lift camshaft raised both torque and power. The
EGR system was removed and the belt driven air injection pump was
replaced with an electric driven pump. The new engine control was
upgraded to a microprocessor type that was re-flashable.
Sadly all of these improvements was not enough; Power went from the
last year AJ6 rated at 219HP to only 237HP with the AJ16. The writing
was on the wall. A new V8 was ready for production and it was cheaper
to manufacture, 12" shorter, lighter, and made 290HP. The death of this
engine was due to the fact that the AJ6 was designed to use the head
off of the V12 (which was a really bad combination), and the spacing of
the head bolts prevented using modern head designs. So in short, in
order for Jaguar to compete a completely new "6" would have to be
designed from the ground upwards. FORDs response: "Here's the V8 we
just made, use it."
So no, the 4.0L does not make an AJ16. It was a short-lived modified
version of the AJ6 that made a AJ16. Very few parts will interchange
between the two.
I hope this answers your question.