Nevermind the post above, I worked out how to stop the DTR pin resetting the basic stamp.
We made a male to female serial adapter with a momentary push button in line with the DTR pin. You have to hold the button down to send the program to the BS2, but the opening / closing of the port that I can't control from within mach doesn't have any effect then.
I know that this info probably isn't really useful to most folks, but I hate finding a post that has a problem just like mine, but the poster doesn't follow up and let people know what worked in the end.
I am still wondering about reading data from the serial port though. I suspect it will end up being something with the modbus, but I don't have time to play with that right now.
The goal of all of this is that the basic stamp allows me 16 extra I/O pins, plus I can enter code into the basic stamp to deal with each pin.