Re: Who's Running the Super Rat?
Sounds like you will need to make a spacer for the base to raise the jug, this will put the piston back below the deck or at least flush with the deck as well as raise the ports so they'll be a lot more open at BDC... Personally I really don't worry about how far open they are at BDC as much as what crank degree they start to open at... More port duration makes for a screamer of an engine if not done too excessively...
Basically when setting up a jug with a spacer it's best done with a degree wheel so you can record where the ports begin to open and from there you can figure out the exhaust, inlet, and transfer duration so you can set up the engine to make lots of power up top without overdoing it and killing off your low end power. Once this is done you can install the right thickness spacer then measure how far from the deck your piston is if it's below the deck, then shave off just the right amount to set your compression ratio and squish clearance.
Then for porting you shouldn't have to raise the exhaust or transfer roofs, but you can clean up the ports and widen them to fit your setup. The intake floor can be lowered to compensate or the bottom of the skirt on the intake side can be raised which does the same as lowering the intake floor to set your intake duration, which needs to be set on the conservative side if you plan on staying piston port.
There's some good power improvements to be had by raising your jug, but you'll need to take the measurements to know how thick of a spacer to make.