I purchased a '04 Freelander a couple months back in non-running condition. Supposedly it just needed a timing belt, but they didn't want to buy the tools after getting the upper intake and a few other things off.
Since buying it I have replaced the head gaskets and timing belt, re-timed it because the cheap timing tools I got needed modification to work and I did it wrong the first time. (In still not positive it’s right, but without better tools to compare to mine I can’t tell.)
Then I found out that the ECU had a short and was melting my #4 coil. One very expensive dealer visit later that is fixed, but the car still isn't running right.
I'm getting codes 1470 and 1477 as well as misfire codes for cylinders #1 and #5.
I have pulled, cleaned, and tested both VIS motors, and both seem to be working fine, I've dropped and cleaned the oil pan (the engine was really sludgy), and restored the shattered vacuum lines with donors from a local junkyard.
The engine idles fairly smoothly, but has no power and accelerates very hesitantly. (In park it takes about two seconds to hit 2000 rpm). I drove it about 60 miles back from the dealer and it made the trip smoothly, but I had a top speed of ~50 mph on flat or downhill and on some uphill slopes I dropped to 20 mph. The transmission slams sometimes, but I can't really look into that when I can barely drive the car.
It smells like it may be running rich, and my timing advance is sitting between 5 and 32 depending on the second and engine speed.
Anybody have any ideas of what to look into next?

 

have you replaced the spark plugs and coils/wires ( coil on cap) ? that made a big difference in mine, double check the VIS motors they have a lot to do with the air flow & thus fuel mix, look into the intake manifold and make sure that the butterflys which the VIS motors are controlling are actually good and operating as the should....not flopping around and blocking the air flow >>>which would cause the lack of power and rich running condition you speak of. there are a lot of you-tube videos showing what to look for there.
the transmission "slam" is likely bad rear diff rubber mounts which allow the diff to move upon accelleration and create the noise and ensuing slam as the diff moves in the rotten rubber mount....there are 3mounts on the rear diff...fairly cheap though.

 

This engine has coils on each cylinder, I'll try swapping them around and see if that changes anything.
The butterfly valve feels like it is moving correctly. It's possible that something is messed up inside, but I can't hear any rattle when I shake the upper intake.
Thanks for the tip on the rear diff mounts, once I get it on the road I'll look into that.