I have a similar but very different setup - A VPI Scout with a Benz Ebony TR to a Linn Linto to a Korg MR200s to Vinyl Studio on Windows. Playback is through JRiver to a Chord Hugo to a Cary SLP-05, Levinson 432 and Sonus Faber Cremona.
The result is everything I had hoped for. The resulting digital playback sounds very similar to the vinyl sound, which just means that the Korg and the Hugo are very good and very neutral. I record at 24/192. We (my wife has the ears in the family) can definitely hear a difference between 16/44 and 24/96, with a much smaller difference going to 24/192. But, disk space is cheap and you only do this once, so I go with 24/192. When I am done, the tracks sound as clean as digital with the sound of vinyl.
A few suggestions on the process, although much of this may be obvious to you.
First, go slow and experiment with 1 or 2 albums you know well. Get the process down before doing a bunch. Figure out what sample rate works best for you. I have several early albums that I ended up going back to because I was too hasty at the beginning.
Learn to split the tracks cleanly. End a track right at the end and eliminate the intertrack gap so you do not have any of the hiss in your final tracks. (Control and left click to move the green line in VS).
Use the Album lookup feature, especially with discogs. It really saves time in getting track names and timings. There are some tips on using it with discogs n the General VS forum.
You can move all of the track breaks from a given point on all at one time, which helps when you have long lead ins or long track breaks. Can't remember the command but it is probably Control and left mouse button or something like that - maybe Alt rather than Control.
Experiment with the rumble, hum and hiss filters. Hum and rumble are easy, but hiss takes a little more thought. Hiss removal does change the audio, but, depending on the album, it really can make a difference, especially on quiet passages. I always do this with headphones and you really can hear the difference. I usually use the gap between the first and second tracks and make sure it does not have any clicks in it. On some albums I use different hiss samples on side one and side two. You can adjust the level of correction if you are afraid of changing the music too much. or want more correction. You can also apply the hiss correction just to specific passages if you want. I usually do it for the whole album. You can see the effect of the rumble correction if you look at the Spectral View in Cleanup.
The click removal is very good, but if you want really clean recordings it can take some time. It always seems to miss a few if the album is not real clean. I listen to the cleaned up tracks with headphones to be sure. Time consuming for albums you care about. After a while, you get a sense from looking at the waveform in Cleanup where the click removal may need help. For some I care less about, I just run the correction and let it be. If I hear something on playback I can always go back and fix it. If the album is very clean and you only want to fix a few places, you can run the correction on just those places and not the whole album. Be careful with the brass correction. II find it somethings misidentifies clicks. I usually do not use it. I do find that some clicks that it does not fix correctly that simply widening the click correction fixes the problem.
Figure out your file structure so that when you write out the final tracks they are exactly as you want them for playback. You can also add silence at the beginning or the end of a track when writing the file, if you want to.
Move you main VS directory to some place that is obvious to you, so you can back it up easily. You can write out an individual track in Split Track - Track if you want to fix just one track.
Back up your original files and your final tracks with an automatic backup routine. I use syncback and do it nightly.
Experiment with RCA and usb cables before you go to far. I did not find much difference, but it good to know early in the process, not later on.
I would run a mono album through the process. Then you can look at the waveform to see how closely he levels are matched. You can also normalize the album with each channel normalized separately. That will give you an idea of how closely the channels are matched and you can adjust accordingly. Even with a very good cartridge setup, there can be differences.
I find that for relatively clean albums that do not need a lot of manual intervention, I can do the VS process in 15 minutes. On some of my old rock frisbees, it can take several hours to get them really clean, with a lot of manual cleanup. That is the price I pay for being careless late at night in my youth.
Obviously, clean your albums first.
Not much help on the actual recording process, since I record to disk and then transfer to VS.
Good luck. I am very happy with the results I get.