Toilet humour - not funny.

Around seven years ago I fitted a new bathroom at home. Well strictly that's not true, the room is the same one, it's everything in it that's new. And as it's seven ears old now that's not true either, but it was at the time.
The project was not without it's problems, and if I was to do it again I'd fit the bath differently and move the toilet a little further over to avoid bare legs coming too close to the hot radiator pipes but all in all I was happy with it.
Yesterday however the toilet cistern stopped filling, and investigation showed that the inlet valve had failed. For some reason it wasn't letting water through to refill the tank.
Dismantling the tank to remove the valve meant separating it from the bowl, no mean feat given that seven years in a damp atmosphere had rusted the bolts that hold it together solid. Even the plastic thumbscrews had seized but they soon yielded when challenged with a blowtorch.
A new valve was acquired for £13 and whilst at the plumbers merchant I bought a new set of bolts. I should have got a new seal whilst I was at it, but I knew I had one in stock in my box of plumbing bits, so didn't bother.
Now there's no delicate way of putting this, so if you are squeamish don't read any further. On occasional mornings we would enter the bathroom to find a small puddle of yellow brown water at the foot of the toilet. Having a small boy in the house we had put this down to a certain lack of control - he's always in a hurry and  his aim might not be good, particularly at night as he hates the dark, and getting out of bed to use the toilet is a trauma he gets over in short order. It seems however we may have been doing him dis-service. The seal was well past it's best and had been leaking for some time hence the water staining the floor. It picks up it's colour as it drips over the rusty coupling bolts. I might owe a certain young man an apology, and a few weeks pocket money he was fined for his indiscretions.
Anyway, with the valve replaced I put the new old stock seal in place, noting that it was a completely different size and shape to the original, but seemed to fit much better. I put this down to seven years being squashed between pan and cistern, but maybe not. Maybe there is a different size of seal, because after many hours bolting and unbolting the coupling and using plumbers putty I still can't achieve a leak free joint.
The tank is simply not a good fit on the toilet pan. I am beginning to suspect that the two components were made in different factories, possibly in different countries and one in metric whilst the other is in imperial, using the inch as the lowest measure. Having looked at the two parts I would conclude that they were designed by different people, who did not speak to each other during the design process. One of them was possibly blind. The two parts are just not destined to be married together. The pan for example has two stiffening webs in the porcelain which are positioned almost exactly in the right place to prevent a spanner reaching the coupling bolts. The cistern meanwhile is designed so that the coupling bolts are directly under the valve and the siphon. And there are only two bolts to pull the two halves together and achieve a watertight seal - no chance. Four bolts in a square pattern would do it,but not two in line. Basic engineering.
So how to cure it? You can't drill porcelain, so adding a further two bolt holes won't work.
I'll try another size seal tomorrow, but if that doesn't work then a whole new unit might be on the cards.
Because at present I've nothing else to go on.