Conrods hitting bottom of cylinder bores

The Barrels appear to have thin liners ,  which  will need carefull  trimming  .

As Robert says, these barrels appear to have liners which new and NOS would not have. Are you sure these are proper 99 barrels? Count the fins to confirm. An 88 barrel on a 99 bottom end would end up withe conrods fouling the sides of the barrels.

Attached photos show underside differences.

The Thunder rods could be wider than the Norton ones.  A dremel  may be  easier to control . Don't leave any  sharp corners for stress cracks to start from.

Its possible that the barrels are New old stock rejects that went in the skip when the factories closed. Staff would go through the skips and rescue stuff . When production problems occured  factories were not beyond  using  rejects  to get a few orders out.  I think thats what my Atlas head was !!. 

Attachment shows better labelled 99 & 650 barrels undersides. All of the factory 99 (& other twins) barrels were machined to bore size from a single casting (number 22709). So no liners were squeezed inside the cylinder bores.  A good engineering company should be able to sort out the cutaway chamfer for you. On the 99 engine the piston rings do not reach to the very bottom of the cylinder.  650 barrels needs more care to detail otherwise the skirts can crack and chunks fall off.

Picking up on Roberts rejects point. Apparently hundreds of Norton engine components had to be scrapped, at Plumstead, in 1963 due to poor machining of the castings. 

So the story goes, when Norton transferred it's production and equipment from Bracebridge St to Plumstead, understandably not many staff chose to relocate, and so a lot of skill was lost.

Several preliminary batches of crankcases had to be scrapped entirely after machining, as the holes were misaligned. In desperation, somebody in management said, "Lets ask Ted (who had operated the capstan drill)".

Ted was duly brought down to Plumstead to see for himself. His immediate question was "Did you bring the piece of wood?" On being met by blank stares all round, he explained that the bearings on the spindle were completely clapped out, having been worn out over many years, but by using a lump of wood to lever the spindles and take out the slack, he could get it to run true enough to drill the cases.

At once amusing and sad, and apparently typical of much of UK industry management at the time in failing to invest in newer equipment when necessary.

I have also read that Norton Built up a sizeable  "war chest"  to invest in a new factory but when AMC found out they  took it to  pour into the AMC  morass.

Don't forget to factor into your gap grinding, enough room for the conrods to move along the big end pins and  still not bounce off the sides of the cylinder slots. Plus at a risk of teaching you to suck eggs, the corners of each slot need a small radius to prevent stress cracking.

Looks a tidy job.  The liners are thicker than they look as they have a decent chamfer on them.

Now polish the edges of the conrods where they used to hit the bores....

Yes this is a fine answer to a problem, I also could not see why this would not work and as Tony says it looks like a badly made/machined barrel in the first place. Now every thing is 'not hitting' but by how much? I would give myself a smidgin of clearance as on the overrun at 6500 in third!! If something touched it could be expensive?? A rough suggestion is to fit the barrels without a base gasket, but with some plaster-scene in the appropriate places, see what happens when you pull them off again? And as DC says any nicks on the rods need polishing out, the slightest nick in the wrong place becomes a 'saw cut' and things come apart-some times in a 'rush'