Maybe you can do it first in Photoshop, then change to Illustrator.
I feel your pain! I work with engineering drawings also and they can be a hassle to connect all the points. I used to select two points at a time and choose JOIN (Apple J). But than the little dialogue box comes up and wants to know if you are going to use a CORNER or a SMOOTH connection. You hit enter and than you still have 3 more corners to go and that's if you're just connecting a square box. A complicated shape can take a LOOOONNNNNG time.
Illustrator doesn't recognize that middle area as anything unless it is an enclosed area. I have found that you can in many cases select all the lines that make up the shape and than click on the first ICON in the bottom row of the PATHFINDER. It's called DIVIDE which makes absolutely no sense but it will connect all the lines together into one shape. It also drops the stroke so the shape appears to disappear but if you will assign a stroke color to it the outline will re-appear. You can also give it a fill then. I usually draw a marquee around the lines I want to select rather than selecting them one at a time. That being said I have not had 100% success with this technique. Sometimes on ROUNDED corners there are so many points that for whatever reason this technique does not work. But it seems to work well in some cases.
What the previous poster suggested would also work. Save the drawing as a PDF or EPS. Open it in Photoshop. Color all the areas. Than save the finished file back out as a TIFF or JPEG and place on a layer under your drawing and viola! All the colors should show through correctly. Resize if necessary although if you rasterize it correctly and save it correctly you shouldn't have to resize it.
Gingersnap and DigitalMan,
In the newest version(s) there is a new feature called Live Paint (Groups) which do(es) paint areas.
If you are using CS4, this should not be a problem. Use the Direct Selection tool to select the lines that form a particular shape. Choose LivePaint under the Object menu and select 'Make' to turn these lines into a LivePaint object. Then, use the LivePaint Bucket to fill the object with whatever color you like.
1. Use the shape tools to draw a few ordinary closed paths, overlapping each other partially. .25 pt. stroke, no fill.
2. Select all the paths. Object>Path>Add Anchor points. Repeat 8 times or so.
Now you have a what looks like enclosed areas, but is really just a bunch of tiny open paths. You've simulated the kind of thing you frequently get from CAD exports.
7. Select all.
Now record an Action that performs these steps:
1. Apply 1 pt black stroke with round endcaps and joins.
3. Apply the Merge Pathfinder.
Everything will look like it just acquired a black fill. But now you have a Group of ordinary closed paths with black fills and no strokes. The outermost closed path completely surrounds the others and is offset from them by 1 pt. (thus, serving as the line work). You can now click the fills of the other paths and apply whatever fill colors you want.
The Action can now be applied with one click.
I frequently use a slight elaboration of such an Action when importing DXFs of exploded assembly drawings. I Lasso or marquee-select around the disjointed paths that make up the drawing of an object, and then run the Action with one click. The result is white-filled closed paths, simplified to remove excess anchorPoints, with a heavier weight outline around the outer perimeter. (Helps clarify individual parts in an exploded drawing--not proper thick/thin treatment, but servicable. Also serves for color-coding by the thick outlines if you.)
The exact best steps to include in the Action depends partially on the nature of the kinds of drawings you typically import; but the principle is generally like that outlined above.
All of this (including workarounds with LivePaint) is, of course, ridiculous workaround for Illustrator's ridiculous lacking any kind of intelligent join command.
Ok, I've tried out both the LivePaint feature and setting up the action script, and they both do what I was hoping for!!! I think I will be able to use them both in my work. Thanks so much for the feedback. You guys have just saved me (and my coworkers) hours of time Glad I asked...