The full terrain protocol was designed to be a pick and run program to make it easier for new users to do it all at once.
You can run it without pause. However, if you find yourself Herxing, you may wish to pause it until your system catches up.
You could extract each step and build it step by step if you wanted, but it may be easier to just stop/pause between major steps as you go.
There is a more comprehensive version of the terrain detox which is Phase 1 of the Morgellons protocol, which takes even longer over 4 generators.
If the protocol guide is still available, you could use the details to perhaps build a detox that is more appropriate for your needs.
I don't think with Rife, there are any shortcuts. If 11 days is too long for you, I don't have many alternative suggestions for you.
Once done, you can repeat it as many times as you like.
For more details, please check: