Well, looking at the image in an online version of the manual.......I see only 3 "bolts".
2 of them hold the valve cover and the 3rd appears to be holding "something" that is concealed by the black cover next to it.
Perhaps you could post a picture (or 2) taken by yourself.
My guess would be that both heads are made identical (to be the same part number) and both have the same provisions for attaching or mounting things. Whatever Deere (or Kawasaki) is using the threaded hole for only needs to use the #2 head, so the same hole on other bank is vacant.

Pic of cylinder head 2 with bolt hole.

Pic of cylinder head 1.

Probably a bolt for holding on the Fan Housing and engine Shrouds.

Pic from online manual

Looking at your picture of head #2 it does appear that there is a "foot print" left by something that was previously mounted there.
The print appears not to be circular (as would be from a washer) and might have been made by a bracket that was bent to a 90 degree angle.
I have looked at both the Deere manual and the Kawasaki manual and I don't see any pictures that show an object attached in that hole.
Your best bet at finding the answer may be to visit the weekend freedom machines web site and post the same query there.

But it's still a bit soon for members here to post their replies.

Have you by chance ever taken this tractor to a shop (or other resource) for any work or has it always been maintained by yourself personally?
For instance, if there was ever a reason the cylinder heads were removed, there is a chance the heads were put back in opposite positions than original. The heads are the same part so transposing them would not be harmful. It would, however, result in that hole becoming vacant and showing a foot print because that same hole DOES secure air duct sheet metal when used in cylinder #1 position.

This post was edited by mownie on Sun, Apr 7, 13 at 12:29

It hasn't been in a shop. I've maintained it since I bought it new. It could have been that way from day one, but I can't say one way or another because I 've never noticed if it had a bolt before.

I have two suggestions. Go down to your JD dealer and asked the guy in the parts department. (I am not talking about a big box store, but a real John Dealer that maintains and sells ALL JD tractors.) If you get there when they are not busy you well get a better answer.

The other is to find a store that deals with used tractors. (Like the one mentioned above) and look at similar tractors to see what the bolt arrangement is.

I worked at Deere dealer for many years.Seems like to me l have seen a lifting bracket mounted there before for installing the engine at the factory.

Just looked at my LT 180 and it is empty on mine too
Guess it's nothing to worry about.

Thanks everyone. You've been very helpful. Looks like it was furnished that way.