I suppose the first question is why you want so many routes to that precision? 8000 routes overlaid on one map is not going to look very pretty. Would you not be better just to draw straight lines? Is the actual route really that important?
There are a number of different problems with the approach you propose above - the first is going to be connecting the rail/subway and road networks together without which it can't be routed as a whole, which from your description above of data with modal interchanges, is what you need.
The next problem is, as you say, getting enough waypoints to force your routes to take a certain mode of transport. I guess you will probably need to get a mid point between each part of the rail network that is between an interchange onto the other network. But how do you stop road journeys routing onto the rail network (which is usually more direct)? You could add a very high cost for rail routes, but this might force some journeys to double back unless you got the waypoint right in the middle. And how on earth do you deal with bus / tram networks, short of adding waypoints for each route segment?
The final problem is processing time. Depending on the size of the network, it could be very high for the number of routes you are talking about here.
To be honest, I'm not even sure that the advanced and expensive transport modelling packages such as TransCAD / EMME3 have this functionality out of the box, as they are primarily concerned with modelled data, rather than real world data.
Bottom line is that it's possible I think, but will involve substantial investment in time to sort out the network and a heavy degree of programming before you can undertake this analysis.
Having said that, someone must have attempted this before. Which is a good argument to ask transport professionals, not just GIS people.
Best Answer
This is a little shot in the dark, but you could use XTools to make points at the start and end of your polyline layer. With the point layer that will be created you could run a distance matrix to calculate the distance from each point to the others. The values will be in distances. There will be zeros (when they are snapped) and large values (when there are far lines). The values in between zero and the large number would be the gaps between the polylines. This approach will allow you to zoom to the specific gap, using the point file.