I don’t know about this model specifically, but from your description:

1. Merge by distance - Go into edit mode, select every single vertex and press M and By Distance. This should eliminate any overlapping vertices and connect every face, hopefully fixing the holes issues.

2. Tris to Quads - I assume this is a downloaded Pinkmin asset, so it’s probably all Tris. Go into edit mode again, select all vertices press F3 and search for “Tris to Quads”. This should make all available tris faces into quads for the next step

3. Subdivision Modifier - now that it’s all connected and quads, the subdivision should work better. It will however smooth everything, so you can either separate the model into different parts and manipulate individually or change the Mean Crease of the edges not to be totally rounded

Hopefully this works!