Usually, fuel change is pretty instant as long as the fuel level is low enough when you fill up, which in you case was certainly low.
One thing to keep in mind is that reprogramming the ECM doesn't always clean out the learned strategy and sometimes it will have to relearn the fuel curves (and shift strategies and idle strategies) a little.
I'm a little confused about what you are meaning by going through the alerts sections. If you could please give me a little more detail, I would be able to better answer your question.
In general, the 97-03 will take about 6 minutes for the first programming session because it has to read stock and build all the files it needs to program. Subsequent programming sessions should take 2 to 3 minutes since they only have to write the files to the PCM. One thing that does take a while is when doing custom options.
Hope this helps.
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