water pump shaft removal?

So you can't get a 6 point box end wrench on that nut with the water pump drive shaft out?? Those 2 shafts , water pump drive shaft and the water pump shaft should be on the same plane, so I'm struggling to see how a box end wrench won't go on, now that the drive shaft isn't in the way.
Also, if the flats on the nut have been gnarled down, your only hope is the 6 point drives, be it a socket or a wrench. you might have to place the wrench or socket over the nut and tap in place to get a better bite on the nut. The tapping may also loosen the nut enough to help free it.
I only break free nuts and bolts with 6 point drives unless I'm forced to use a 12 point or open end wrench because of access issues, but if I have to use an open end wrench, I won't push it to the point of damaging the flats. Just too much experience having to deal with issues like this.
Let us know how you make out please.
KB

Post script
A picture of the access for the water pump shaft from the bottom side of the cylinder block. Just for reference.





 

unfortunately I only have two 12 point (ring) and open end combination spanners. I don't think I have ever seen 6 point ring spanners but if I don't get it removed once the block is off I will take the block to my trusted professional bike shop.

I do have a spare nylon bevel gear if it comes to the point where heat has to be used but not 100% sure it was for A1/2 engine with pickups behind block - I reckon I'm about 95% certain as it has the extra cog to drive the timing pickup shaft

It's too bad that most young men that want to do mechanical work are not advised to buy 6 point wrenches and socket sets BEFORE buying 12 point wrenches and sockets. The price difference is negligible and why they even produce 12 point drives is beyond me. Almost every manufacturer of tools offers both but what you commonly see on the shelves at the stores is 12 point drives. Pathetic!!
Do you have 6 point sockets in preferably 1/4 inch drive ??
I still struggle to see how the access is limited with that shaft out of the way.

This image I managed to grab from a previous post but what it depicts is exactly what happens when you try to break free a tight fastener with 12 point drives. 12 point drives only bear down on the corners of the fastener and will always damage the corners such that the bolt or nut should be replaced rather than using again.  Snap-On specifically made their wrenches and sockets with reliefs in the corners of the wrenches and sockets so that their tools could not damage the corners of the fasteners. The only drawback to Snap-On is the price of their tools. $$$$. and one would argue that you get what you pay for. They call it their "Flank Drive System" ( and no, I'm not rich enough to have Snap-On tools)
Snap-On Flank Drive System

 

I treated myself to a new open flare spanner but that did not help. There just isn't good access to the nut from above. I took the block off and found that a 6 sided long reach 3/8" socket is a near perfect fit between the nut and the rear of the cam chain chamber., It's all out now and a new flanged nut has been ordered
When I have a problem nut I would normally go for 6 sided socket in preference to 12 sided or open ended 
 

Glad to hear that you managed to resolve the issue. Obviously, the pics I was referring to  are from a different engine casing and I now can see your dilemma. Tight spot for sure. Kudos !! Hope it's all down hill from here. if nothing else, it was a good opportunity to talk about the advantages of the 6 point drives. Thanks for that.
KB 

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AvE does a good test of 6 point vs 12 point box wrenches and comes to the conclusion there's no difference (at least for good quality wrenches on undamaged bolts).