
The first thing that rings bells with me is why an initial run when you arrived. The change of filter was obviously going to effect things. And a standard filter chucked back in but still no needles or mains changed yet. Then all of a sudden it's we can't use the BMC lets stick with stock.

The guy is sort of right about the free flowing air filters but not totally, yes the VTR airbox is extremely sensitive to tuning and does not like being messed with, but that does not mean that it's not possible. Plenty of people run a K&N or other aftermarket filter's it just means that it's not a straight swap and it takes some dyno time to get it dialled in accordingly. Seb is correct in what he's saying. That is the whole point of a dyno. Otherwise you may as well stuck with the stock settings which is near enough what you are now running with the exception of the needles.
So once it's decided which filter to use he has then changed the mains and put the needles in, and then done another run. IMO what should have been done is to change the needles, mains and filter first of all and then done a run. There are example base settings with the FP instructions that could be used for a starting point. Then go from there. Pete is also right and the larger main should be in the rear to help keep it cool. Surley even logic should tell him that as the larger one was in the rear to begin with.
With regards to the drilling of the carbs, I don't know why he has not bothered with that. Maybe it's something he did not feel confident with. Yes once it's done you can't go back, but if the worst comes to the worst then 2nd hand carbs are on ebay all the time averaging £50. He could have given it a go and then used the dyno to get the carbs dialled in accordingly. I don't know of anyone that has taken this route but I'm sure FP know what they are doing and the reasoning behind it. Just seems a bit of a cop out to me.
Saying that though, with the dyno read outs you have it's giving out good bhp but that's not everything. Looking at the last chart (4th gear HP & Tq) the torque curve is reasonably straight. There's a couple of little dips, one at 60 and then goes back up at 70 to 80 then there another little stutter at 90. But overall pretty good.
The A/F reading is a little on the lean side at the start then tails off at 5.5. It's not totally sh1t and 14 is optimal performance but these bike like to run on the rich side a bit so would be better nearer the dashed line on the readout. This would also explain the hesitation. I think to mixture is to weak with only 2 turns with the 45 pilots. With 48's you would find about 2.5 turns out would be about right. And why is the mixture the same for front and rear carb when they have different mains. TBH I would expect a dyno technician to adjust the mixture by ear which is the more professional way of doing it. Also this would not take up time having to remove carbs to adjust again. On the top end mains the A/F run back onto the lean side which makes sense as he gone smaller than standard with one of the mains.
The other two charts are little more all over the place and I can't work out which one is of importance so I just following the last one. I'm wondering whether he has just done it in a way to give you good max BHP and not specifically to the A/F throughout the whole range.
In all honesty and by going by the last readout it's not all bad and a very reasonable readout but could be improved a bit. I'm a bit myth'd to why he just did not dial it in with the BMC, K&N, standard or whatever filter you give him to use, that is the whole point of using a dyno. And why he put the larger in the front just makes no sense especially as with the standard Honda setting the larger goes in the rear. Did he check the emulsion tubes to make sure they have not been changed or been put back the wrong way around in the past at all.
If I had my own dyno I would start with getting the mains that gave best performance with a slightly larger one in the rear, then move onto the needles and then the pilot jet/mixture screws.
OK I have rambled on a bit there and I don't want to make you feel worse, but that''s my opinion. I would see how you get on with it and maybe go back to them in a few days next week or whatever and tell them your not entirely happy with the way it's running and get them to richen it up a tad, specifically the lower end if your getting that lean hesitancy. What you want to achieve is as straight a line as possible along the dashed line on the A/f scale. If it's going to tail off at all it's better to go on the slightly rich side than lean so towards the 12.
(:-})