It’s great that you have worked your way through the material.
In regards to, “At this point I’m wondering if there is a comprehensive step-by-step program for building up my alternate picking skills. Something with Basic, Intermediate, and Advanced levels.”
The Downward Pickslanting portion in Pickslanting Primer is actually already what you are looking for.
Under the Yngwie Malmsteen section refer to the “Alternate Picking - The Pop Tarts Lick” and “Building Speed With The 6 Note Pattern”
Just practice these two exercises (The first 6 Note Pattern will be easier since there is no string switching) until you can shred them both; then move onto the next 6 note positon/variation.
These two exercises appear overwhelming at breakneck speed but are actually just patterns, and both use alternate picking. The Pop Tarts Lick is longer so break this down into smaller sections. Please kindly refer to my first post on this forum for a complete breakdown on exactly how I did this.
Completing the Pickslanting Primer alone at a respectable level will likely take me an entire year of practicing every day, not even counting the complete Volcano, Cascade, and Antigravity seminars. Who knows how many years that would take to master? By that point just about anyone would be at an extremely high level of technique…then there are all of the interviews and live events to go through.
It’s tempting to look for the ultimate guitar training, the good thing is that you already found it. Stick with it man!