There aren't many good reasons to tune a Jawa.
One of the most common complaints about Jawa mopeds is the unreliability of the stock ignition system. The 207 and 210 engines both employ a simple contactless electronic ignition system (the forerunner to the modern CDI). The thyristor unit is prone to overheating, resulting in erratic or absent spark. A replacement unit can be soldered together from component parts. Some experimentation has been conducted http://www.mopedarmy.com/forums/discuss/1/537594/499438/
There are no bolt-on pipes for Jawa.
You could possibly hack most right side pipes with a little work.
The stock exhaust port is very small and you will have to move the exhaust studs.
Stock Jawa port timing is pretty okay but the ports are really small. The stock cylinder has a cast iron liner so it should be pretty easy to modify the ports.
There are several piston sizes for the 207 and 210 engines. As the stock cylinder was worn out it would be bored. Each rebore increases by 0.25 mm. In the United States pistons were available up to the 3rd overbore, but pistons as large as the 8th overbore (an increase of 2 mm bore and 7 cc displacement) have been found in eastern Europe.
Jawa cylinders consist of an aluminium jug with with an iron sleeve pressed into it. This sleeve can be pressed out to give better access to the ports for modification. The 210 cylinder is superior to the 207 cylinder due to its two additional angled transfer ports. It also has a larger flange around the exhaust port making it easier to modify for a larger header. This cylinder can be bolted to the 207 engine with no modifications.
There is a commercial rototiller that has an engine which is a derivative of the 210 engine, allowing access to 80cc cylinders.
Additionally you could always weld up the cases and move the studs to use a different cylinder, considering the small end bearing size and stroke.