Hi Chris,
Can't help with the command line interface to the COM-port, never seen that before. Doing serial coms in VB.net using the supplied serial port object is quite easy though. Just beware that Microsoft removed the serial port object from VB when they introduced .net and put it back in some later version. I believe all the Express versions have it if that's what you're using. It's been a long time since I played with VB.

On the PIC side there's no problem to receive "any" number of bytes. HSERIN can split the bytes up properly as it receives them or, if you're using an interrupt driven routine you can store the data in an array and split them up when everything is in. It all depends on how the data is formated, high or low byte first etc.

/Henrik.