Playing old .wrk files (containing MIDI tracks) in Sonar X1

You could drag and drop the old midi data on to the new soft synths midi track.

Are you inserting your soft synths as "Simple Instruments tracks" or as split Audio/Midi tracks?

You were headed in the right direction the first time, but when inserting the synth, you need to choose to create the track for the First Audio Output (or All Outputs - Stereo if it's a multi-timbral synth). Then re-direct your existing MIDI track(s) output to the synth, and you should hear them. If the synth is multi-timbral, you'll want to set a different output channel on each MIDI track, and assign instruments to those channels in the synth GUI accordingly.
 
If you don't have SONAR create the output tracks(s), you can add audio tracks after the fact, and assign their Inputs to receive the synth output. I actually recommend creating tracks and assigning their I/O manually to start so that you understand how MIDI Track > Synth > Audio Track routing works.
 
Simple Instrument tracks which combine MIDI and Audio tracks with automatic assignment as I/O to/from the synth, are appropriate for non-multi-timbral instruments, and you can preserve the clip start times by holding Shift as you drag them from the original track into the SI track.
 
If you have a lot of similarly arranged projects to convert, you might want to create a template project with all the usual tracks and synths already set up, and copy the MIDI tracks from the original project into a new project started from the template.
 
Regarding missing low bass notes, a lot of bass synths/patches are programmed to sound an octave lower than notated to make it easier to record MIDI from a 61-key keyboard. You may need to transpose those tracks up an octave (or use the non-destructive Key+ offset in the MIDI track). If both low and high notes are missing, you may have played beyond the range of the instrument.