First off, you dont gain compression by raising the cylinder, you lose it, and you lose alot because your gaining the entire 69mm of bore area to added volume.
Second, if you raised the exh. port you will have lower compression then when you started, the port now opens sooner, and for a longer duration because of the raised roof.
Lastly, if you have a cpr head, you have a head that has lowered compression on the mag and center cylinder, the pto cylinder is already lower on a stock viper, he simply opens up the other 2 to match the lower one. So to gain back compression it all depends on how high the exh. port is and what the squish clearance is, the bigger the squish, the lower the compression. You dont ever want to raise a viper cylinder because the transfer ports are way hotter in port timing then they need to be anyways, if you raise the cylinder more you had better be spinning the motor to 10,000-12,000 plus rpm. Make it easy on yourself and have a educated path to follow by simply checking the squish(there is a post on how to do this in the tech section by myself), once you have numbers to work with you can easily see whats right and whats wrong with your current combo you have there.