I am not sure what you want to use the baja for. Different engines are available to help fit the application your plan to do. It sounds like your looking for top speed though, and a 2mm stroker engine is not the best choice for that. IMO, from all the engines I have worked on, I would not chose any 35mm bore cylinder. Some people like them, and the 27cc stock stroke engine can run pretty darn good, but they have quality issues that I don't deal with and that head kit 29cc 2mm stroker engine is probably the lowest reving engine out of all the RC engine possibilities. It does have good low end power and a pretty strong mid range, but there is a bigger cylinder out there with a bit better quality that beats it everywhere. There are plenty of top end kids that will bolt up to your cases, and all three cranks will bolt right in that don't cost over $200.00. If top speed is what you want---first get rid of the stock exhaust--it hiders all engines a lot. IMO, a G260 Zen engine or top end with a good pipe, and if you want to go all out--a reed kitted top end that is well built can make more RPM and power everywhere.
Here is a page from DDM with quite a bit of options. Check it out. All of the two bolt top ends will fit your stock cases, accept for one I build for a replacement top end on TS reed cases.
http://www.davesmotors.com/store/headkits.html