Great to hear from you and on your guitar journey.
Sounds like you have great motivation and are enjoying it and putting the work in.
My first guitar was also a yahama from ebay.
Hope to hear more from you
Your guitar is good for a starter.
There pain in the fingers are natural, and practicing every day is great!
You might want to split the 2-3 hours per day into smaller times of 3 to 4 30-minute sessions.
Playing for about an hour will surely deliver the pain in your fingertips.
As you develop the callus in your fingertips, the pain will be lessened.
And even with callus, your finger will definitely hurt with playing for more than an hour.
Keep on playing.
Hi Nathan, welcome to the community. Good you are already playing some songs you like. It doesn’t hurt checking on other learning resources, but I think you should stick to Justin Guitar method a your main learning path. I do not have experience with acoustic Yamahas, I have an electric, but I think that if it’s allowing you to learn what you have learnt so far and the songs you are playing are sounding good, upgrading you guitar is not an absolute need. One think to check is the action (distance from the strings to the fretboard). Although I have also an inexpensive guitar I took it for a setup one year ago and the technician corrected the action. It has been a lot more enjoyable to play since then (some would say to spend the money in a better guitar, but more expensive guitars also may need a setup; although, sometimes is included in the price by some guitar stores)
Nathan, Welcome to the community forum. I second the advice to get the action height checked and split up your practice into smaller sessions. More than 1 hour of playing is heard on beginners fingers until you get calluses.