Part A
No the chamber doesnt draw anything out at the very beginning on export open. At BDC is where the chamber pulls hard on the transfers. There is no 'shock' wave in a pipe there is 3 waves pressure, particle and sound. We can't pick the difference but pressure moves the fastest, followed by particle and the sound. Yes you want the reflection of pressure to arrive back at the exhaust port as it is closing. By the time the transfers are fully open exhaust gases should be long gone.
Moding the piston or rasing the transfers does the same thing just 2 different ways of doing it.
Read the ESE tuner thread on Kiwibiker from about pg 450 onwards and you get some valuable info it's always there to refer back to. A good tip to find something on a 800pg thread is google " ESE Tuner transfers Wobbly Frits Overmars"
Yuou get this
http://www.kiwibiker.co.nz/forums/showthread.php/86554-ESE-s-works-engine-tuner/page657
