You can get real deep if you want, there is a lot more involved especially when it comes to grinding ports. Its as much as art as science.
Avoid upping the compression too much, kills entry speed, harder on motor internals and is less forgiving with jetting.
Simply advancing the ignition statically will probably end in tears, there are mod ignition boxes with custom curves, thats probably a better route.

If you wanted a quick pick me up, I think leave the ports as they are, reduce the cylinder head vol a smidge, get a “mod” ignition CDI that has a curve to match your pipe and cylinder. Of course, having done that you will need to re-explore your jetting setup and moving to a higher octane fuel is probably not a bad idea either.

Building a good Mod Honda is a science as McMahon has said…  It’s lots of things and they all have to work together…

You can’t “bore” a nikasil cylinder without replating it, and it’s not legal in any kind of karting….

Case prep was a big part of it, porting the cases and cutting and welding the kick starter hump for a straight intake would probably make the biggest change, along with a good pipe and a stock 99 ignition advanced all the way, run a TM 125 piston, shim the cylinder up, and tighten the head up.  That’s the way Banke had us run them until he came out with the programmable ignitions, albeit with RS125 pistons…

All that and the stock Honda guys will still be faster!!!!  :)

CR

Port the cylinder, port the cases, reconfigure the head, cut the kickstarter boss for a straight intake, build a pipe to match your porting, cut the choke section out of a 39pwk weld the snout back on and bore to 42mm, dry sump your transmission, cut your clutch down to 3 disks, develop exhaust water injection system, and you will be close.  Or fix your stock honda and have fun.