I wouldn't bother boring that cylinder. You'll pay around $80 to do that and then how much is an o/s piston and rings? You'll have as much or more in it as a new kit.
are you getting most of your info from the FA50 performance wiki page? That article is unclear on many things and needs to be supplemented/changed.
Contrary to what the article says, I don't believe that increased compression increases power across all ranges. More likely just low end.
I've never owned an fa50 but I've ridden one once. ha ha! Anyhow Honda and Yamaha restricted their engines in at least one way. With the piston at bottom dead center, you'll see it still partially blocks (in the Honda Express, for example), all the ports. I'd have to look at the Yamaha but I know the piston still partially blocks at least the exhaust port (3-4mm worth). I would bet Suzuki did the same thing since these bikes were subject to various states' laws limiting top speed.
What the wiki article might be trying to convey is that if you take a metal spacer, shaped like a base gasket, you can use that to push the cylinder forward. The piston will still remain in the same place but the cylinder is pushed forward. So if you take a 1mm spacer and sandwich it in between two base gaskets (that are 0.5mm each), you have pushed the cylinder forward 1.5mm (you only need to account for one paper base gasket and not both). I wouldn't use the alternative of a bunch of paper base gaskets stacked on top of each other. I assume but don't know that there are metal spacers available for the fa50. And I'm telling you to just take two aspirin at a time, and just because they helped that doesn't mean take the whole bottle. So don't get a 4mm spacer and throw it in there and think you'll set the world on fire.
Remember the piston stays in the same place. So if you move the cylinder forward, the piston will no longer reach the top of the cylinder at TDC. So you have to mill the cylinder the same amount you pushed it forward (1.5mm or so depending on how much the paper base gasket compressed). You don't need to mill the head unless you want even more compression which will lead to more problems than solutions.
Now you've exposed 1.5mm more of perhaps every port in the cylinder. Doesn't sound like much but in the world of small engine 2 strokes it can be huge. You'll want to up jet as well.
These changes with the stock crappy exhaust won't amount to much but with a performance exhaust, you'll notice a nice improvement. I had a machinist mill the cylinder for $20 plus postage. They usually want inch measurements rather than mm.
Here's my Express in beast mode after these simple changes were employed: