I recommend reviewing
Scientific Method. It is process used in pretty much all engineering and research & development projects. Note important step is gathering empirical objective data and analysing that data to see if results are what you anticipated. Then formulating new plan to steer project towards your goal.
Read these texts on internal-combustion engine theory and tuning. Basically 1st-year FSAE background stuff before we got hands dirty with actual engines. I have all these on bookcase, can loan them to you with deposit. Best stuff I've ever learned.
Internal Combustion Engine Fundamentals - Heywood 1988 McGraw-Hill
Engineering Fundamentals of Internal Combustion Engine - Pulkrabek 2003 Prentice Hall
Flow and Combustion in Reciprocating Engines - Springer, Arcoumanis, Kaminoto 2009 Verlag Berlin Heideberg
Performance Tuning Theory & Practice - Four Strokes - Bell 1981 Haynes
Tune & Modify Automotive Engine Management Systems - Hartman 2004 MBI Publishing
Motorcycle Fuel Injection Handbook - Adam Wade (click for freebie chapter).
Thing is... you don't have to re-invent the wheel. Millions of racers have taken this path before you since 1986 and done exact same trial & error process. All you have to do is look at their results and replicate their steps. I got my 250 up to 110mph top-speed (122 on dash). Racer_X got his Bonneville bike up to real 123mph (136 on dash). You'll want to examine experimental data and results of anyone you're talking with about upgrades. Do they have measurable results you're looking for?.
Heck, Spears was one of original racers of these bikes back in 1988 and is more knowledgeable than
anyone I've encountred. And I've met at least 100 racers who've modified these things extensively with engine-boring upgrades, casting their own engine-blocks, along with EFI conversion, nitrous/methanol injection and turbocharging!
