In a nutshell:
Jury-rigged = GOOD
Jerry-rigged = BAD
from WordOrigins.org :
Jerry-built, meaning to temporary or shoddy construction, dates to 1869. It may derive from the name of a builder who was notorious for poor construction. An 1884 source (unconfirmed) says that the phrase is in reference to a particular construction project on the Mersey River in Britain.
From Etymonline.com :
jerry-built
1869, Eng. dial. jerry "bad, defective," a pejorative use of the male nickname Jerry (a popular form of Jeremy), or from naut. slang jury "temporary," which came to be used of all sorts of makeshift and inferior objects (see jury (adj.)).
However, we should not confuse "jerry-built" with "jury rigged". While they sound similar, their meanings are DIFFERENT.
According to WordOrigins.org:
Jury rig, while similar sounding, has a slightly different meaning, emphasizing the temporary nature of the solution and can imply an ingenious solution done with materials at hand. Jerry-built, on the other hand, is often used for a permanent, but poorly built, construction and has no positive connotation.
The origin of jury rig is nautical and dates to 1788. It is from the nautical term jury mast. This term dates to at least 1616 and refers to a temporary mast erected to hold sail when the normal mast has been lost due to storm or battle. It is commonly thought that this sense of the word is a clipped form of injury mast, but no evidence of this longer term has been found.