Hello Michelle,
I believe you are correct in your guess that the internal clock will not appear the PCLK terminal until the VI is running. For burst handshake I/O protocol, PCLK can be configured for an input or an output. PCLK can only output the internal clock after it has been configured to be an output and the VI must be running in order to carry out this configuration.
Yes, you can simultaneously have group 1 (ports 0 and 1) configured for output and group 2 (ports 2 and 3) conifgured for input because there are two groups of timing/handshaking lines to control each group. If you would like to see an example of this and are using LabVIEW, take a look at the following example.
http://venus.ni.com/stage/we/niepd_web_display.display_epd4?p_guid=B45EACE3F06956A4E034080020E74861&p_node=
Hope this helps,
E.Lee
Eric
DE For Life!