You are over thinking it, which I think is common for most people starting with megasquirt.
A great way to start is just to set up megatune and the correct code version on your PC, don't even connect the megasquirt, then browse through all the menus and features in megatune. Use the F1 key to learn about the features.
Then load an msq file from someone that has a similar setup so your engine will start. Turn off accelleration enrichment and tune your VE table using a wideband. Then turn acceleration enrichment back on.
Then over time start to learn about tuning after start enrichment, warmup enrichement, spark table, using target AFR tables, using autotune, etc
The most basic things you need to know going into tuning for the first time are:
1. What AFRs do I want as I tune all parts of my VE table
2. What spark timing do I want in the spark table
BTW, once you browse through all the options in megatune you will answer some of your own questions, like the rev limiter.
Here is something: You set the number of cylinders your engine has in the constants tuning page. You set the rev limit in the rev limiter page. So engine is 8 cylinder, rev limit 6000. Or engine is 4 cylinder, rev limit is still 6000. Don't worry about math, just enter the parameters you want in the tuning pages. Save yourself some gray hairs in the beginning. You can worry later when you try to tune your spark table as close to detonation as you can get.