[Embo]

Is part of the delay in having his jersey retired the fact that he was (rumored?) estranged from the university after the way the school treated his dad as coach?

That was no rumor.  Elway had been quoted as describing President Donald Kennedy and AD Andy Geiger - the two he felt responsible for his father's firing - as "those two clowns".  It was only after both had left (Geiger in 1990, Kennedy stepped down in 1992) that the thaw began.  I did read that John and his family were in one of the press box suites for Big Game 1999 to see the clinching of the Rose Bowl berth.  He was also frequently in the stands to see his daughter Jessica and the rest of the WBB team during March Madness. 

[Embo]

Is part of the delay in having his jersey retired the fact that he was (rumored?) estranged from the university after the way the school treated his dad as coach?

That was no rumor.  Elway had been quoted as describing President Donald Kennedy and AD Andy Geiger - the two he felt responsible for his father's firing - as "those two clowns".  It was only after both had left (Geiger in 1990, Kennedy stepped down in 1992) that the thaw began.  I did read that John and his family were in one of the press box suites for Big Game 1999 to see the clinching of the Rose Bowl berth.  He was also frequently in the stands to see his daughter Jessica and the rest of the WBB team during March Madness.