Increasing compression will likely gain horsepower, though there are multiple ways to go about approaching this. The easiest way to add compression is to deck the block or go with a thin head gasket, both ultimately reducing the squish band (the outer portion of the combustion chamber where the piston comes closest to the cylinder head). But a thinner head gasket isn't always an option, and a lot of times, we do prefer to cut the block so that if we lose a customer – if he moves across the country or something – and he has somebody service his motorcycle, that person could just put a stock part back in his motorcycle and not have a problem.
Of course, every engine builder is going to have their opinion on what squish number is best, and for a supersport class engine you'd want to run it on the safe side. For me, I know the customer is going to be running this for a year or so before it's inspected again, so I wouldn't run the squish number as tight as I would for a engine that's going to get rebuild after a few race weekends. You can take material off the cylinder head, though the effect can be less due to the shape of the combustion chamber. Taking material off of the cylinder head will also affect cam timing, as will a thinner head gasket. Cam timing is another way to manipulate power. In certain regards the cam timing is less important than getting compression in the engine. Some people think it's a fix-all for everything, and in old times it could give you more power, but now it more just moves it. Unfortunately, it's also kind of a black art and takes a lot of dyno time. And it depends a lot on other things, like your exhaust system or intake, those things.
That's an important point too, that there's no single change that is the magic change. All of these changes work in conjunction, and it all has to be a complementing set of numbers. Still for most engines especially like one for a customer, we did install cam sprockets and change the cam timing. And with that, there are some sweet spots where engine builders will want the cams to do their thing. But again, this will vary between engine builders. Of course, any gains here will only be truly seen when the motorcycle is put on the dyno and properly tuned, the fuel-injection mapping and ignition timing allowing the builder to fully exploit the benefits of each.
Every engine builder will pay attention to smaller details as well, ultimately setting bearing clearances where they want them to be and replacing things like rod bolts (it they are stretch bolts) or modifying the slipper clutch to make the slipper function better. For me, it's all coming out anyway, so I'll go through the transmission and inspect the transmission shift forks and shift drum, making sure to replace any worn or damaged transmission bits. Same for clutch plates, you know, if needed. And at that point all of the gaskets are getting replaced, some of the seals are getting replaced if there's sign of a leak. I put manual cam chain tensioners in ever trackday or club-race engine too. They just keep all the parts moving relative to one another in the time span you want them to. It keeps the cams in the location relative to the crank because if there's big wave – like if a guy is aggressive with his downshifts – and the chain is loose, it will put a bunch of slop in the chain and the cams could potentially flop the other way, and now you could possibly go into collision. With valves hitting the piston.
In the end, there are near countless things an engine builder could do for added performance or reliability, and these main areas are just the tip of the iceberg. How far you want to go depends on the rule book you plan/need to base the build off of and how much you want to spend. Keep in mind though that every change you make will need to complement the next, and that the other real important part here is the inspection and replacement of necessary parts for added assurance as you roll out for your next race.