I have posted a fair bit in various threads most have dropped down the order now there is a TR Polarised Thread.
There is a lot of good information in the older threads, and I don’t mean by myself. There is also the normal $*£%^&. to sort through… 
I’ve answer some of your questions here…
and (and the post below, scroll down)
The shorter intervals less than 5 minutes I’d tend to do a 2 sets, an example 2 sets of 4x 4’
I don’t think I’ve ever done the 4x 4’ session, it has always been 6-8x 4’ or the 2x 4x 4’ just mentioned.
If a TTer I would progress longer Supra-Thresholds sessions extend them to close goal event time, otherwise I’d focus more on the punchy, Breakaway and Rouleur efforts 5 - 10 minutes and then start increasing the power and or start sitting closer to FTP in the recovery valleys.
Generally I like to keep the hard days over 105% FTP but never do these intervals based on FTP. I use the PDC and take ~92 - 95% as the target.
Getting event specific do the intervals and then just sit on FTP as long as possible (a total killer to be used sparingly before a good taper)