I'm sure some others with more experience could add some more specific details, but I'll give you my understanding and opinion. Increasing the compression is probably the one thing that will substantively increase torque and horsepower across the power band, i.e. through all the RPMs, especially off the line. Stock, the clone compression ratio is like 7.9:1, meaning the entire volume of the cylinder and head when the piston is at the bottom of the stroke compresses from 7.9 "parts" down to 1 part. A flat (rather than the stock dished) piston and a 14cc head changes the ratio to 11.8:1, which results in a more "violent" explosion, so to speak. Most high performance engines have much higher compression. 14cc is the volume of the combustion area in the cylinder head. The stock head is 22ccs. Check out this chart.
http://nr-racing.com/manuals/gx200comp.pdf Most other modifications tend to be a trade off of one sort or another. Modified cam shafts tend to improve performance in certain parts of the power band, depending on the exact cam. Bigger carbs, big valves, head porting, etc., tend to focus on improving air flow and make power in the upper RPMs. Needless to say, this is very simplistic and there are a whole lot of variables, but you could bolt on a 14cc head and see immediate improvement in accceleration even with the governor intact. Get adventurous and add a billet rod and flat piston and you'll be even better. The only difference on my GX200 is I added a mild cam and removed the governor. I also added some parts for reliability rather than performance, e.g. stainless valves, pushrods, billet flywheel, etc.