I think the best bet is to do a series of hand-drawn strokes to fit different situations, and use them as anchored objects. You can set the positioning for the anchored object as part of an object style applied to the various strokes, so when you copy and paste into the text they will at least position themselves correctly.
I see no way to accomplish this without a lot of manual labour. Anchored objects are a good way to make the underlines move with the text, but I think it would go faster without anchored objects. If you go this route, then make sure the text has been proofed, reproofed, and re-reproofed.
You could use a custom underline defined as part of a character style in a spot colour as a marker. Use Separation Preview to show only that colour then draw over the underlines in the same colour wit the pen tool or import artwork created in something more suitable such as Illustrator or Photoshop. Use an object style for the underlines so you can make global changes easily and put them on their own layer so it’s easy to manipulate only the underlines without accidentally clicking on the text. When you’re done, change the character style to remove the underline and edit the object style or original artwork to get rid of the spot colour.
Thanks for the suggestions. The text in the letters is static and the client has told me that there will be no changes to the format or the copy within the letters. So I don't think there is any benefit to anchoring the underlines. Although that is a very helpful suggestion if the lines had needed to flow with the copy. At this point I have found that the fastest way is to just draw a simple line with the pencil tool and stretch or shrink it to fit the sentences that require the hand drawn underline. Luckily the client has already underlined the sentences that he wants to look hand drawn so I can use them as a reference and then just turn them off. That was my original plan and I can finish a letter in about 10-15 minutes. Its a shame there is no way to edit the wavy underline option, because I think the client would go for that if it were a little more inconsistent and flat.
Thanks again guys.
Here is something that can be done to create an irregular and rough underline.
It is done with a combination of underlines and strikethroughs, using a custom dash stroke. Then create a character style to be applied. You could even create additional character styles, offsetting the underline different values.
I am not suggesting that this replicates a hand drawn shape, but it can be used to create a rough underline.
This doesn't look terribly hard to script.
Let's say you started by underlining all the characters that you wanted underlined, and also you created an image (in Illustrator, photoshop, or whatever) of the underlining for a row.
A script could walk through all the lines of text, and find each range of underlined text. It could then place the line-length image underneath that range of characters, cropped such that it does not extend beyond them. It would do this once for each range in each row.
This would, of course, need to be entirely redone any time the text was edited. But that doesn't seem too bad.
You would have a single image placed in your document thousands of times, but that doens't seem bad either.