Well, basically, for this project, I spent the first day and a half just capturing like a mad man. I made a spreadsheet of the games I wanted to include and just went for it. I try to capture in chunks per console since each machine has its own quirks in terms of how you capture it (I use the OSSC for 240p and 480p but can only play 240p on my PVM so I have to use an external viewer for 480p which is annoying). For 480i, I use the Framemeister instead since I feel it does a better job with interlaced signals - the bob de-interlacing on the OSSC is somewhat less attractive (though I did wind up using it for Hydro Thunder on DC since I could not get VGA support to work on that game and didn't want to swap everything for one title).
Once I have all the necessary capture I film any b-roll (though I didn't need to do much here) then write the script. I find that I usually write in chunks - I'll write up the first 5-10 minutes, record the VO then start editing. I waste too much time if I write everything in one go due to writer's block at times. I usually start with the introduction. Once I feel that setup is good enough, then I move onto the meat. I'll edit in all the clips I already have and make notes of any extra footage I might need.
From there it's just a matter of editing in chunks - once the first 10 minutes is polished and looking OK, I'll get back to writing and start working on the next chunk. Moving back and forth between writing and editing helps keep me moving forward. For most retro videos, though, I tend to film myself to improve production quality which means I need to write more of the script. In those cases, I'll nail down the first 15 minutes or so, then imagine where I'll need filmed cuts and write all the transitional segments and the ending. I then bring that up on the teleprompter, setup the camera and lights and film that.
So it's really just a matter of assembling all the assets, making assets for comparisons (in some cases), filming b-roll, writing, filming on-camera stuff and editing. I usually have a pretty good idea of what I want an episode to be in my head. The big challenge is always pulling it off on time. I'm pretty good at estimating how long each episode will take but usually have to make compromises. I can't always go into detail on things I might want to and sometimes I have to decide not to film myself (I wouldn't have had time for this one). Each day is usually 10-12 hours of non-stop work too. So three days means three FULL days.
Well...believe it or not, the only footage I used from previous capture was Panzer Dragoon 1, that small clip of Powerslave, and the MGS2 stuff. Oh, and the modern games - like Sea of Thieves where I needed a quick clip. Other than that, everything else was fresh capture since I needed specific clips. With Tomb Raider, for instance, the clips I had left didn't showcase the water so I had to re-capture that. I haven't featured Sonic R before either so that was all fresh.
I do capture most content with a Shogun Inferno and the files ARE massive indeed. I archive some but not all of that footage. For the stuff I keep, I have no choice but to compress it to H264 MP4 and store that. It's not perfect but it's good enough in a pinch. Otherwise I couldn't possibly store it all.