I've been doing AS/400 performance anlayis for over 20 years, and I can tell you that the approach you are proposing is a fairly difficult way to go about obtaining response time data. The TN5250 datastream is relatively complex, and you may find it harder than you think to use protocol analysis as a mechanism for monitoring response time.
IBM offers built-in performance monitoring and management tools. Why not just use those? It is possible to monitor interactive response time in real-time, and through batch reporting.
The free, IBM-supplied performance collection utliity, Collection Services, has the ability to capture detailed job performance data, including interactive system response time and a bevy of other useful performance data.
You can use IBM (Performance Tools, Job Watcher, etc), third-party, or homegrown tools and queries to analyze the performance data that is collected.
In addition to providing transaction response time information, Collection Services can track hundreds of other performance statistics on interactive, server, and batch workloads.
Here's a short PDF that discusses the various performance tools available to AS/400 system administrators.
http://www.redbooks.ibm.com/redpapers/pdfs/redp4026.pdf
- Gary Patterson
Check out my EE profile: http://www.experts-exchange.com/M_4382324.html 
