blue wrench

Regarding the timing belt guide, make sure there is an air gap between the guide and the timing belt. There is actually a spec for this, and there is a handy tool from Gates, but if need be you could probably use a piece of cardboard. Wedge it between the belt and the guide while you tighten the bolts down, remove it when you're done. If not done, it can and will rub/damage the timing belt.

Just a thought about your powdercoated p/s and a/c brackets, the alternator might ground through them. I don't remember for sure though, just something to keep in mind if you see problems with the battery charging.

Maybe it's just me, but your pics don't seem to be completely backing up your post because it looks to me like 2 different crankshafts pictured. For example the pic with the long block assembled appears to show a black/hardened crankshaft, but in the pic with the yellow cloth it's not black and the crank also looks used, you can see the old marks left behind from previously installed rear main seal and oil pump seals, doesn't appear to be a new crank.

This would be a good time to unscrew the banjo bolt that feeds oil to the turbo and inspect the filter inside. Clean it, replace it, or remove it. Is this on the 08 Legacy? If so then you may also need to replace the top section of the oil feed line that bolts to the turbo and the lower coolant hose, due to different lenth/fitment from the stock VF46.

It may still be worth checking out if the production date of your car was close enough to the 05MY. If you can pull your glovebox you will see if the access hole is there or not.

I don't know exactly what the deal was with the following, but almost all 05 Legacys I have worked on did not have cabin filters when I came across them during a major service. The compartment is there it was just empty and it did not have the access hole to easily reach the cabin filter, you need to take the entire glovebox panel off. The later years do come with an access hole covered by a bracket and some dash fabric. The reason I mention this is because the lack of cabin filter causes the evaporator to become plugged with dust,dirt, etc. And does not allow to the temp sensor that is installed right on the body of the evaporator to read accurately. The only way to really check though is to completely pull the evaporator from the dash. Yes it is very doable in the car, no dash removal required. It isn't the most complicated job but it's not exactly fun if you're doing it for the first time because of the cramped space you have to work around.

Have you pressure tested the coolant system? If not, have a shop take a look at it or purchase a tester and check for yourself. Also for the record, removing the intake manifold is not necessary to reach the throttle body coolant hoses.

Looks like the contact from an ignition coil, lives inside the boot.

Seems to me like the vertical lines are just deposits of material from the pads, but hard to tell exactly from the pics. The rotors also have some grooves forming and decent amount of rust buildup on them. But I agree regardless, needs new rotors. I've also never heard of that brand myself, but looking at that rust it seems like a good idea to spend the extra money on a kit with coated rotors.

Looking to upgrade to a Grimmspeed TMIC, either version (thermal coating or bare). If you happen to need a stock TMIC, I'd also be interested in a trade + cash (stock top mount with about 20k miles, purchased new in 2018 from Subaru).

Being a non-turbo engine, all of those items are not bad to reach should you need to replace them afterwards. The PCV valve is cheap enough that you might as well replace, and it couldn't hurt to clean the oil control solenoids while you're there. Everything else shouldn't be a problem. Do clean the throttle body though, easy to see straight down since you have the manifold off now, and on a similar note, clean the MAF when it's all back together.

You should only have to remove the nuts/washers holding the engine mount studs to the engine crossmember. The mounts will come out still bolted to the engine.

I think you have the right idea by removing the aftermarket remote starter to begin with, just to rule that out all together. As far as getting no response from the starter, look into the 'security relay' and its circuit. This was a while ago so I don't remember it exactly, but I believe the security relay is what controls the starter relay circuit, and is signaled by the ECM. With the vehicle I found this on, it was a matter of narrowing it down to the ECM itself, after finding no problems with the security relay itself and its circuit. Used ECM fixed it.

There's a couple of ways you can go about it. If you have some time and money to spare, you can finish removing the control arm from the ball joint stuck in the knuckle, and order yourself a Subaru ball joint puller tool. Snap-On makes one, as well as Company23, and there may be others. If you have access to an air hammer with a chisel bit, you can also try placing the edge of the bit at a downward angle, on the lip of the ball joint that protrudes when it's in the knuckle and air hammer it out. With 2 people, one person can place a long pry bar between the top of the control arm and the bottom of the knuckle (where the pinch bolt goes), while the other person swings a BFH to the control arm right by where the ball joint stud goes through. There's a chance you can beat the control arm to hell this way, but a non issue if you're replacing the whole arm. With any method, it can also help to VERY CAREFULLY spread the knuckle apart, where the pinch bolt goes through, with either a chisel and hammer or air hammer.

Is your turbo right? Id be interested to see a pic of how you have it mounted with the oem intercooler.