Hello Pat,
You are close. Ideally you need to worry about the LIS datasources as they work on the push delta mechanism. Coming directly to the point, process of clearing up the delta queues is quite simple.
1. Lock your system for users.
2. Run V3 jobs (should be in SM37 or you can run manually in SE38). Programs to run in SE38 based on your list of SMQ1 queues are: RMBWV302, RMBWV303. These will clear up the extraction queues (starting with ) that you see in MCEX* and put the data in Delta queues that you see in RSA7 for each datasource.
3. Run the datasources in SAP BW system at least 2 times (better 3 times).
4. Check the entries in RSA7 - Total column should be 0. If not then repeat the steps 2, 3.
5. Delete setup tables from transaction code LBWG before upgrade.
For Generic/ FI extractors follow step 3 only, this will cause delta queues to be cleared. Generic extractors and FI extractors as they extract data directly from tables have pull delta mechanism. That means for generic or FI extractors data is always present in Delta Repeat queues so you don't have to worry about it regarding moving data from SMQ1 to RSA7. So When you run the extraction from BW system your SMQ1 queues for generic extractors will also get cleared up.
Generally upgrades cause problems if there is data in delta queues so simple rule is:
1. Clear delta queues by running BW extractions(infopackages) in BW system for all datasources.
2. For LIS datasource specifically clear extractions queues(MCEX*) in SMQ1 too.
Please let me know if this helps.
Thanks
Amit