This is where we sit:
Looking at the engine from the front, the coolant temperature switch (left sensor) was relocated on the 3.5L so the wire for the switch needs to be extended. It's a single wire, so not a big deal.
The exhaust manifolds from the 97+ 3.0L are the same as the 3.5L. The exhaust pipe and Y-pipe are not the same. The 3.0L y-pipe has a slightly different angle on the legs and is a inch or two too short on one. The 3.5L pipes are not usable in the pre-99 Sports. The newer pipes have CATs built in and uses O2 sensors installed before the pre-CATs.
Everything on the front - brackets, ps pump, air conditioner, etc. bolt on to the 3.5L from the 3.0L. Timing belt and plastic timing belt covers are different - the 3.5L belt is longer. Since everything was virtually new, we just transplanted almost the entire front of my 3.0L onto the 3.5L engine.
The throttle body from the 3.5L has a completely different configuration for cruise control, different IAC and different TPS. The good news is the 3.0L throttle body is a direct swap. Throat diameter appears to be exactly the same as the 3.0L from my '97.
The motor mounts and motor mount engine brackets are different. The 3.5L mounts and brackets are both longer (taller) than the 3.0L mounts and brackets. How this work, I'm not sure. The block width appears to be the same, so.... In addition, the 3.5L engine brackets are positioned about 1/2" forward of the 3.0L engine brackets. The 3.0L engine brackets are not a direct bolt up to the 3.5L engine. Looks like the solution is to use the 3.0L motor mounts and 3.5L motor mount engine brackets. Snip the bracket off the base plate, cut it down to the correct height and relocate it about 1/2" towards of the rear of the engine. I'll have definite information on this once we drop the engine into the bay for a test fit.
Oil pans are not interchangeable due to the longer stroke of the 3.5L. The pan assemblies are the same height, but the lower section of the 3.5L pan is longer and extends further towards the rear of the engine. This is just a suspicion, but there may be clearance issues with the sub-frame on stock IFS 97-99 Sports. (see the weird motor mount stuff above) The primary issue here is that that extra couple inches sticking back may limits the upward travel room for the track bar and drag link on SAS'd Sports.
Now the sucky parts ... <img src="/forums/images/graemlins/frown.gif" alt="" />
The starter ring on the flywheel is about 1/4" smaller in diameter than the 3.5" flexplate starter ring and the flywheel starter ring sits about 1/4" further away from the back of the block than the flexplate starter ring does.
The 3.0L flywheel bolts to the 3.5L just fine and the height from the block to the face of the flywheel is the same on both the 3.0L and 3.5L. No issues with bolting the clutch and bell housing up.
The starter through 1998 is different than the starter for the 99-2004 and are not interchangeable. We tried my '97 starter on the 2002 3.5L flex plate and it doesn't engage. We then tried the starter from my 2003 3.5L and it works perfectly. The 3.5L starter is PN M379687D.
The bell housing backing plate for the manual transmission is different than the backing plate for the automatic transmission. Both will 'fit', but the manual transmission backing plate leaves a bunch of sizable gaps between the engine, oil pan and plate. There's a tiny gap when using the automatic backing plate behind the flexplate access cover on the driver side of the engine but a very small amount of gray RTV applied before installing the cover will fix that. The gap is REALLY small.

SO, now I'm kinda at a stand still. I have a complete engine ready to drop in and no way to start it.

I would welcome any advice on this!!
Edward