I think that if you rotate the engine some more, the lobes will be facing the correct way (180 apart) at the real TDC.

 

It seems that I noticed, what you are describing, one time when I was checking my valve clearances. I think your cams were in there correctly, otherwise your engine would not run.
You not only have to be at the TDC mark on the flywheel, you also have to be in the right part of the cycle at TDC for the cams to be oriented correctly, and the T mark to be in the inspection window.

 

I would agree with dan888. You have to visually confirm tdc with valve cover off. If cam was backwards, did you rotate again to T? It takes few rotations and PASS T few times to be at true tdc

 

Make sure the lines on the cam gears are parallel to the top of the head. that's TDC

 

Was the exhaust cam also upside down? With the "T" lined up, you could be at either the top of the compression stroke or the top of the exhaust stroke.

Ride on
Brewster

 

How tired or otherwise stressed were you when you started this job and discovered the problem?

 

If you leave the crank alone, unbolt the cams and reinstall them correctly, you will find that the ignition is now off by 180, so I would say just leave it. Don't fix what ain't broke.

 

Well, I have reviewed the photo I took and it definitely looks wrong to me.

There is a noticeable deference in the way it starts and idles now with no other changes.

I would like to make sure I am not retarded. I turned the engine over by hand multiple times and enjoyed the awesomeness that was an upside down intake cam. I took the pic as soon as I noticed and was a little past TDC.

If I am retarded just call me out.

 

OK, all kidding aside... You have a 4 cycle engine, it takes 720 degrees to complete the cycle. One rotation is 360, you have the engine at TDC, but your at the top of the exhaust stroke, not the compression stroke. The cam rotates at 1/2 the engine speed.
Rotate the engine another 360 degrees, or the next TDC position and see what it looks like. There is no way your engine is running with the cams not timed with the engine/ignition.
I think all the above posts (or mine at least misspoke on the 180 degrees out).

 

The 180 degrees are in reference to the cam, not the crank.

Ride on
Brewster