That's the missing piece of the puzzle. You should transcribe some Phil bass lines, note-for-note. (And for extra credit, transcribe what Jerry is playing, too!)
This will build your skill set to follow your guitarist when he goes off on a musical tangent.
I play a lot of Dead music and this is what I would recommend.
Pro tip: If you are just starting out with Phil, 70's era Phil Lines are a lot easier to learn/transcribe than early 80s and beyond Phil lines. I generally find anything beyond the early 80s to be generally inaccessible from a playing standpoint. By that point he had been playing with two drummers for many years and was really throwing some crazy bass lines out there.
Listen to some 72-77 Phil and draw ideas from there. What I usually would do is just pick a section of the song, loop it and play along with it till i figured out what he was playing.
Im not sure whats going on in that recording but something sounds off initially. I don't think it's you either. It sounds like he changed keys than switched back.
Easiest thing to do is just ask what key he's improvising in before you start playing.
