Compress TiVo Files?

I suspect this has been covered well in the past but I'm a Johnny-come-lately and I haven't found the answers yet.

I have recorded analog TiVo for years at basic quality and was satisfied with the picture quality and file size, some of which I archive for later viewing.
Now, my cable company is going all-digital so the resulting files are about 10x the size of my old analog files. I upgraded my Series 3 HD TiVo to a (used) Series 4 with a 4TB drive so now my "new" TiVo can hold enough programs before overwriting them.

But the huge digital HD files are going to be too much for my NAS so I'd like to compress them. I experimented with TiVo Desktop Plus and find the iPad setting produces files comparable (in size and quality) to my old analog files. I experimented with VideoReDo but haven't broken the code on that yet (guess it's time to read the book).

So here's what I'd like to know:
(1) Firstly which file types are compatible with the S4 TiVo such that I can reload and play them on the TiVo? Or put another way, what file types should I avoid?
(2) Second, What are the recommended transcode settings to get the best quality/file-size tradeoff? I haven't tried pyTiVo yet but I have tried kmttg, VRD, and Desktop Plus and they all have a set of predefined transcode options.
(3) Finally, is there a significant transcode speed difference between the various tools?

Thanks in advance for whatever insight/experience you may offer.