4. Bare ruin'd choirs: —A choir is a group of people who sing, but also a space in a cathedral. It's "The area of the church between a transept and main apse. It is the area where the service is sung and clergy may stand, and the main or high altar is located." Below is a photo of a choir in the choir of Wells Cathederal in England.

Starting in 1536 (28 years before the birth of Shakespeare in 1564), Henry VIII dissolved the English monastaries, seizing all they possessed. As a result, many monastary churches fell into ruin, and began to resemble "boughs which shake against the cold." Below is an example, Tintern Abbey, painted by J.M.W. Turner about 200 years after Shakespeare wrote his sonnets.

4. late: lately.

10. that: as.

12. that: i.e., the ashes of what was formerly the fuel.

14. ere: before.