Bike after major service

So I had the valves done at 38k (VFR800 2003 model) and after two weeks where I was on my holidays the bike came back to me in worse condition then I left it. The reason it went to the garage was some weird knocking behind the right air vent when it heated up after 5 minutes ride. The mechanics suggested that since it have never had the valves done and it's over 25k it would be a good time so I agreed.
As to the weird knocking as someone suggested on this forum I asked the mechanic to change the oil as the knocking started straight after I changed it myself. So they changed the oil for a different brand 10w40 and the knocking disappeared. Everything would be great if they didn't get to do the valves.
After the bike came back to me and I rode it for a day I found the oil pressure light was faintly blinking every now and then for a couple of seconds when the engine got hot. Also the temperature was going way above 105C which it never did before. This was only when the bike was hot and not moving with engine started like when parking or on lights. More than that my ear caught some different faint knocking. This time it was when at 1500RPM. When I set the revs exactly where I hear the knocking I can hear it repetitively about every second maybe 2. According to my invoice they did 2 shim buckets, 6 shim valves as apparently they couldn't do anything about 2 of them, all valves clearance adjustment, spark change, oil and filter change, and coolant.
So the bike went back to the garage. They were puzzled about the uncontrolled temperature rise and the oil pressure warning but as to the knocking they suggested it's some flap on the air-box which it wasn't doing it before because my air filter was so dirty. I'm green when it comes to bikes mechanics knowing only some general stuff but this sounds like BS to me. Is any other VFR doing the knocking at 1500RPM. Funny that the flap would open and close itself every second at constant RPMs.
Anyway, after 3 more days at the garage the bike came back to me. It had yet another oil change and I was suggested that there was some dirt on the oil pressure sensor (funny it wasn't there before). They've apparently eliminated the knocking which funnily after two days riding I can hear again. And otherwise everything is supposed to be perfect which funnily again is not what I sense when riding the bike. But all that extra work was free of charge.
I cannot see a point in going back to that garage yet again. I wonder if anyone here could suggest either that the knocking is indeed normal for this bike or otherwise what could that be before I get BSited in another garage?

 

If you could record the knocking a youtube video ,perhaps someone here could help.It is generally hard to diagnose a sound.There was a rider here posted about loud whining noise on 5th gen engine and after posting the video it was determined that it was normal.
I am not saying yours is normal but without real evidence about the knocking its hard.

 

Makes sense. Tried doing that with my phone before but even I couldn't recognize it as being the same what I could actually hear on the bike. I'm just waiting for a Gopro so I'll try that and post a link if it sounds anywhere close. Probably reising the tank woudln't heart but it's full now so I need to do some miles before I can attempt that. Shouldn't be long as it was burning a tank in 100miles before the service so if adjusting the valves didn't help it'll be only a couple of days.

 

I can tell you that you do have a flapper on top of your airbox. I took mine off shortly after getting my bike but I do seem to have been able to hear it now and then opening and closing. If I remember right it is on there to control intake noise.

 

Over-heating after a coolant change could be air in the lines, not bled out properly.

100 miles per tank, something is making it run very rich. Fouled O2 sensor, dirty air filter, a defective temperature sensor, etc. Run the check engine diagnostics to see if any codes come out.

Fuel injection systems typically control the idle speed by adjusting air flow with a flapper valve or some sort of air valve. 1500 rpm could be a high idle or a barely cracked open throttle, maybe the computer is having a hard time to know the difference, i.e. throttle position sensor out of adjustment. Just some ideas to consider...