also the recording sounds muffled.
It sounds muffled compared to you listening to the tape player on headphones? Or muffled compared to the way you remember them?
Windows machines can try to help you with sound transfers. It naturally likes processing voice for conferencing and chat. It doesn't like music very much.
Did you make any special Windows settings when you set up to do the transfers?
what format should I save as?
Archives should be in WAV (Microsoft) 16-bit, Stereo. That's music CD format.
You can get a little relief with Lossless Compressed FLAC, but most people want the tiny sizes you can get with MP3 and other compressed formats. You can do that, but those come with restrictions and rules. You have to guarantee you'll never want to convert the MP3 shows to anything else. Musical damage increases when you edit or convert an MP3. There are some special MP3 editing programs which don't increase the distortion, but they don't have very good tools and effects.
For example, if you wanted to create a music mix for a party or gathering, the music from an MP3 archive isn't going to sound as good as the original tape transfer. It may be good enough, but you need to know it's going to happen.
There is one compromise. You can create archive MP3s at super high quality, 256 or 320 instead of lower "normal" quality. This quality will degenerate slower if you need post production (but it still gets worse). This is a trick that ACX AudioBook uses for its voice submissions.
You can make a WAV into anything else at any time with little or no decrease in quality. That's what you get for those large files.
Koz