A few thoughts:
1. I think the Bloomingdale and freight corridor segments just west of Western Ave. have the most ridership potential. I'm not so sure about the 40th St. corridor between the existing Orange and Red lines.
2. While your plan seems sound in concept, there are several complex engineering challenges, to wit: At the point where the Bloomingdale portion turns south onto the existing Metra ROW to Western Ave. is a busy interlocking (A-5). This segment would certainly need to be elevated, and preferably curve onto the west side of the ROW to head south, where there appears to be a little more room to support such a structure; according to Google Earth, anyway. It would be great if this route could get closer to the Western Ave. Metra station so it could be better served, but the elevated curve south to the Western Ave. corridor (where it would follow UP's Rockwell sub initially) has to be built at least a block or two west of the station, if it's going to be long and smooth enough to maintain speeds of 45-55 mph. The Green line transfer station could work here, but your map includes a pedestrian walkway to the Metra station. That's simply too far.
3. Speaking of which, excessive distances between routes and/or modes for transferring purposes would also apply to the proposed station at Pink/BNSF. A better solution would include the Metra station on BNSF at Western Ave. being reconfigured so that it could border the "Navy" line to the west and its namesake street to the east. The Western Ave. Pink line station could also be adjusted in the same manner, and could be easier to do logistically since you wouldn't have to get the blessing of a class one railroad to do so. No doubt, it will still add to the price tag, though.
4. Today, there are five routes (Brown, Pink, Purple, Orange, Green) using the Loop elevated and it is quite busy, especially during rush. And the Red line is CTA's busiest route, with trains operating on 3-4 min. headways during peak periods. So, with both existing downtown routing options pretty much maxed out in terms of capacity, I just don't think there's any way this line could be routed efficiently into the Loop. The only alternative is to build a new dedicated subway that runs under the Red or Brown lines just north of the Loop and links up with the Blue line subway somehow to share the existing downtown stops, not sure offhand how that would work. While the Blue line subway can support additional trains, it could complicate the routing, and add even more to the price tag. Modifying this route is a better idea, and with that in mind...
5. It may be best to modify this line into a "semi-circle" route (actually looks more like the number 7 in reverse when viewed on a map) with a West-South orientation (or North-East if you prefer), with service between the Clybourn Metra station and the existing Orange line station at 35th/Archer, while truncating the other part. Both proposed terminals would provide transfers to existing services, and the new route would be kept out of downtown. If something like this ever got built, it could be a great compliment to Chicago's transit network, but it absolutely must be done right in order to realize the full potential...
--Dorian--