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?

The KV6 is mystery to me, so can't help, but well done on what you've achieved so far!

Low compression caused by valves bent because incorrect cam timing procedure is very common on the KV6.
Low performance is likely due to incorrect cam timing. The KV6 is a very fast revving engine, when it's put together correctly.

I'd be doing a compression check on all cylinders and post up the results.