It is certainly possible that something, either the frame or the engine, was a little 'skewed' from the factory and someone had to push a little harder to get it assembled. If that was the case, it would explain everything including your inability to reassemble the system now.
As far as something being 'warped', that is possible of course. It is also possible that a hole was drilled in the wrong place in the engine (we cannot tell which one(s) are off, only that the last thing to go together will not align) but I think that is unlikely. More like that the frame is off somehow.
As far as the flexing of something to allow the engine to align as Chet had mentioned, I don't think that is happening. The engine is very stiff and will not bend or warp into a new shape easily. The frame is more flexible but still it is a box- section and very rigid and not likely to be moved appreciably, or not enough to cause mounting hardware to misalign, with nothing but the bike's weight on it. A couple of people on board with the bike bouncing off of speed bumps for example and the frame might flex but not just sitting on the ground with the engine removed. At least in my opinion of course.
As to the engine being a stressed member, it certainly is on the C-14. The frame section is like the letter "C" with the open ends pointing toward the ground. The engine crosses the open points of that "C" and ties the ends together to become like the letter "D", or a stirrup on a horse saddle. Once the engine is bolted across the open ends of the frame the whole assembly (engine and frame) become very rigid and the engine itself serves to stiffen the frame (hence the term 'stressed member' because the engine is acting like a turnbuckle inside the frame and not allowing the ends to flex). The front motor mounts serve to attach the engine to the frame on the forward leg of the "C"; without them the engine would hang by the rear mounts and the frame would be able to flex too easily.
So assuming nothing moved when you removed the forward engine mounts, and there is not enough clearance in all of the engine mounting holes put together to realign the mount, and also assuming the front left mount was too tight to begin with, I believe you only have two choices: the first is to put the mount back on the bike by using enough force on the bolt to get it started and then tighten it. That is risky because it might gall, seize or cross- thread, all of which would be bad. You can go a long way to keeping the bolt straight by using a tight fitting socket and long extension but there is still some risk. The other method would be to remove a small amount of material from the motor mount bracket to effectively move the hole location. You could do this with a router or a round file by hand, in just a few minutes. Again, just remove enough material to allow the mount to be installed without any undue force on the bolt, not enough to make the bracket flop around on the three bolts before they are tightened. It is up to you which way to go.
You could also try getting something done under warranty but I really don't see the mfg. replacing either the engine or the frame- I think a dealer would just lean on the bolt and force it home, and then say everything was fine. Because the bike is apart it is also pretty likely that there will be some question as to the source of the problem, the owner or the manufacturer. This is always a practical concern when bringing something that is in the middle of being worked on and claiming there is, and always was, a warranty issue somewhere in the middle of the basket of parts.
Best of luck and please do let us know how this goes.
Brian
OK
Let me say that when I read the words 'adjustment collar' in the manual I got all excited, only to realize that they are not part of the solution at all. They only serve to reduce the clearance on the rear mounts to 0mm between the engie and the frame so as not to stress the frame when the rear bolts are torqued.
As you may remember from geometry, you cannot change the angle of a triangle without changing the length of one of the sides.
The three mounting places in the engine casting are our three 'sides' in this triangle, two in the rear and one in front.
In order for the engine to move down in the front to line up the holes, the engine would have to pivot around the center axis of the lower rear mount.
It cannot, because that would change the distance between the upper and lower rear mounts.
There is absolutely NO adjustability between these three mounting holes. They are fixed in place by the holes in the frame, and the holes in the castings of the engine.
On the inside of the front mounts, you can see threads were carved into them on the upper surface when the bolts were
threaded through at the factory.
The only possibility is that there is enough flex in the upper frame to allow someone to force the engine down while the frame is held in place, which would allow the bolts to line up properly with the frame.
I don't know the sequence in which this bike is assembled, but I can imagine one that would allow this to take place.
For the record, the holes don't line up on either side, but it turns out that it is the right side which is slightly worse.
I also am not sure of the purpose of the front mounts, as the engine is held very firmly in place by the rear mounts. I am guessing it has something to do with the overall rigidness of the frame, as they would prevent the frame from flexing upwards at the front of the bike.
Still at a loss as to how to get them to re-align. I think a giant pry bar from the front onto the head is the only thing that would work.