Back at it over the weekend. I figured out some of the new harness. The Control Pack manual lists connectors that can be removed, so I found and tagged those. I don't think I'm going to tear into the engine harness too much until the Control Pack arrives. That'll be the real indicator of what gets plugged in and what doesn't.
The coolant temp sensor wiring will clearly need to be "un-harnessed" and moved. Here's the old sensor location on the right compared to the new one on the left. The connector is on the right where it would connect before.

That one isn't major surgury. I already separated it from the harness, and the wires it was bundled with are on the "remove" list.
I've got the intake manifold roughed on, and the alternator in place, and I wanted to do another engine test fit. So that was this afternoon's activity. Definitely everything got tighter with the alternator on.

Just what I feared - the alternator is pretty well competing for the same space as the original engine mount. I really wanted to leave that in place and unmolested, but I think it's going to have to come off. I will probably set up the alternator on the mill and see how much I can take off the mounts before they look like they belong on a Lotus. There's a lot of metal there, but I might be able to gain a 1/2" or so.
Either way, I can't really go forward of the motor mount, and I can't really go behind. I think it's gonna get torched. I'll measure them and make a 3d model so that if for some reason I ever want one I'll have the info.
Top view of the same:

Here's the top view. It's just too much of a conflict.
I had another bracket to deal with - this one held the old electric fuel pump:

That one was interfering with the intake manifold. At least this one just bolts on. Unfortunately the bolts were buried in the driver's side foot-well behind the steering rack. Couldn't even see the nuts! Got one off by braille, and couldn't get the other one more than a little loose. I ended up hack-sawing the other bolt from the engine side.
I'm not actually clear on whether that pump was factory or added later. This car has a lot of questions like that.
On the turbo side, I will probably be doing some rerouting of oil and coolant lines, since the factory hard-pipe sticks out more than I'd like. We'll see what kind of room I have once the driver's side clearance issues get resolved.