I don't think that I have missed this, but exactly what is the make and model of your MD unit. With this information I/we can look up the unit and tell you exactly how best to lock everything together.
Another thing that has not been mentioned is that when Sony first designed the MD system --- (did so because Philips designed the CD system and every CD or CD player that Sony made/sold, they had to pay a royalty to Philips)-- they designed it to be one step better than CDs of the time --- they made it recordable (just liked the then popular cassette tape system), but because it was digital it was possible to do a direct transfer to another MD unit without loosing quality as you did if you went from CD to cassette.
Because record companies were (even then) having problems with piracy (ie people buying a CD and then running off cassette copies for their friends, etc), Sony built into the MD recorders a copy protection system that allowed one only copy transfer if using digital copying, this protection was added to the copied MD with the result that if someone tried to copy the copied MD it would not copy.
I say all of this because if you go from your MD unit (which will have recorded the protection onto the MD when you first recorded it) to another MD unit or another device in digital format, it is quite probable that you will not be able to do anything with the copied file.
However if you go analogue from the MD unit to whatever then this copy protection does not come into operation and you can copy, edit, or whatever to your heart's content.
Being the current owner of four MD players/recorders and having used MD units professionally since they were first released if you use the analogue output from your MD unit (especially if it has "Line Out" rather than Headphone Out" and you set the correct levels on your input recording system (reaper, audacity, DAW, whatever), then I will almost guarantee that you will not notice the difference between copying in digital or analogue format and a couple of analogue leads will be a lot cheaper than having to purchase a digital interface, TOSLink optical cable, optical input card for your PC, etc.
I have done this analogue copying system for more almost 25 years for radio station broadcasts, super professional live theatre productions, client song copies, singers backing tracks for their live performances, etc and I have NEVER had a complaint that the audio quality was not good enough.
One final thing to remember is that there are two optical audio formats, the Sony TOSLink format (two channels of audio --- ie stereo left/right) and ADAT optical (8-tracks of audio for multitrack recordings) AND THEY ARE NOT INTERCHANGABLE, even though the optical cables can look the same, but even there there are two TOSLink cables, the difference being the plug at the end of the cable --- one looks a bit like the bumpers at the end of a rail-way track, the other looking a bit like a 3.5mm plug but with a hole in the centre to let through the optical light. But either type is expensive compared to an analogue cable and if going optical be sure to get GOOD quality cables, cheap ones often will fail completely or will not give good results and be sure to get the one accepted by you MD unit and whatever it is going into.
David