The reading of voltage and temperatures can be done with an analog input task.
Your pulses should probably be done with a counter.
So, yes, you can do those with a few DAQmx tasks.
I am using a flat sequence structure (two frames for both states of the pulse) to create a timer. I wanted to use that to create boolean states to drive the PF digital outputs. Would that be possible while the analog task is executing?
Yes, that is possible. However, given what you have described as your intention (create digital pulses), there's no need to create a timer and digital pulses yourself.
The 6341 has built in counters that can be used to generate digital pulses via the DAQmx API. DAQmx includes a few examples of how do to this, located in the NI Example Finder:
1) From any LabVIEW window in the menu bar, select Help » Find Examples...
2) Navigate to Hardware Input & Output » DAQmx » Counter Output
I'd start with the Continuous Output or Single Pulse Output.
This did help quite a bit. I was able to create two tasks. One handled all of the input and one handled the digital output.