Congrats on getting to work on your first visual novel!
I'll be glad to answer your questions!
1) I use a wacom cintiq to digitally draw everything by hand. Everything is drawn in photoshop. Some of my older works were drawn by mouse though (the original sprites I uploaded).
2) While I'd love to draw male characters, I'm so bad at them right now due to not studying the anime style proportions enough that I just don't draw them. I am working to gather a lot more resources to try and work on being able to but I don't forsee getting them on the level of my female sprites anytime soon. I'm really sorry about that!
3)Over the past 5 years I've collected a bunch of links to sites with free resources of all kind. Here are some of my favorites that provide both BGM and SFX:
Pocket Sound
https://on-jin.com/
https://www.tam-music.com/
Good luck with your project!!