I'm very sorry to say this but you're going to have to remove all the tiles and start over. You will never been able to prevent this from leaking fully.
It may also mean removing and replacing the backing as well.
The critical step you missed was the waterproofing membrane that goes under the tiles and in and over the drain pipe. The tiles don't stop the water at all but are for aesthetics only (and to protect the water proofing). What makes the shower water tight is a sturdy backing covered with a water proofing membrane like liquid flash (one I used) when I did my tile shower. http://www.constructionchemicals.com.au/products/waterproofing-membranes/
But there are many different brands. They are a paint on product and very easy to install.
Don't expect your tiles to be waterproof. At best they are only splash resistant. Water goes right through the grout and can also enter around the side of the tile where the grout is. Porcelain tiles aren't quite as porous as ceramic, but most wall tiles are ceramic because they are a lot lighter. These tiles act like a wick and just draw the water through to the back of them. If you don't fix this you could be in for some serious mould issues down the track.
Unfortunately there is no simple fix to this but to start over. I would not recommend just trying to seal it. It's like covering up rotten wood with paint, it won't last and won't fix the problem long term. Although you've got water resistant plasterboard. It won't last long term. These plasterboards are just designed to repel water to keep it out of the gypsum they are made of, not designed to be constantly wet.
Interesting construction that your builder used water treated plasterboard + chipboard for the construction. 6mm or 1/4 in thick concrete based tile & slate underlay board + waterproofing membrane is all you would have needed. I wouldn't recommend tile on plasterboard at all. Even with the layers that he has. It's not as strong.
Since I know how much work goes into these DIY tile showers I will say this. If you feel overwhelmed, call in an expert. They will have the job done in a week and you'll be able to move on with life. But if you're up for the challenge and want to learn to do it right this time, then dive in and go for it!
Best Answer
If they aren't hexed holes then they aren't replaceable, you might have to put a hex bit in to confirm removability. It sounds like you removed too much. If the seats were scratched, pitted or therefore defective, then you should've put new good ones in instead, if possible or returned the taps. But, you shouldn't touch the seats unless or until they leak & if you do it should just be a light few turn honing.
If the seats started out like most seats, being proud or raised from the shoulder, but are now flat or even with the shoulder. Then, you took way too much off. Only the seat is your seal, not the entire shoulder. You'll either need to get new seats, if they remove. Or, have to go to thicker washers. Or, get new taps with replaceable seats & not touch the included seats.