Today, despite widely available technology such as high-resolution scanners and printers, counterfeiting is more difficult than it was at the time of the Civil War, when it was estimated that one-third of all currency in circulation was counterfeit.
A. Today, despite widely available technology such as high-resolution scanners and printers, counterfeiting is more difficult than it was at the time of the Civil War, when it was estimated that one-third of all currency in circulation was counterfeit.
Correct.
B. Despite widely available technology such as high-resolution scanners and printers today, counterfeiting is more difficult than it was at the time of the Civil War, when it was estimated that one-third of all currency in circulation was counterfeit.
Incorrect. The comparison becomes awkward. "counterfeiting is more difficult than it was in the past" begs for a "when?". Today should be referring to counterfeiting to make the comparison clear.
C. Despite widely available technology such as high-resolution scanners and printers, counterfeiting is more difficult than at the time of the Civil War, when it was estimated that one-third of all currency in circulation was counterfeit.
Incorrect. Same problem as B.
D. Today, despite widely available technology such as high-resolution scanners and printers, counterfeiting is more difficult than when it was estimated that one-third of all currency in circulation was counterfeit at the time of the Civil War.
Incorrect. No need of two conjunctions (than/when).
E. Today, because of widely available technology such as high-resolution scanners and printers, counterfeiting is more difficult than it was at the time of the Civil War, when it was estimated that one-third of all currency in circulation was counterfeit.
Incorrect. It changes the meaning (e.g. even though versus because).