Hi, Littlemoe!
Filling in the holes in the bottom of the hull is completely up to you. Unless you pose the tank on its side or upside-down, nobody will know!
The Tamiya "gunshield" (mantlet cover) plastic bag suggestion is best avoided! It is commonly acknowledged in hobby literature here in Japan to be a very poor way to represent the mantlet cover. And I've seen pictures to prove it! I used the nice Ordnance Models resin piece on my M-41, but I've seen some really great covers made by hand with a variety of putties. AFV Club also sells a vinyl mantlet cover for 400 yen (about $3.60 US) if you can find it. I'm not sure if it would fit the Tamiya kit very well, though.
The tracks do have a "proper" way to be put on; with the "pointy" end of the semi-triangular pad pointing down (looking at the vehicle from the front). Be careful if you have the kit with the box art showing the tank from the rear! You may confuse the direction of the tracks if you mistake that to be the front of the tank (and it's easy to do!).
As far as painting the tracks goes, I left the AFV Club tracks the original black and drybrushed dark metallic gray on the metal parts (everything but the rubber pads), then washed and weathered 'em.
The Tamiya tracks are already a metallic gray color, so you may want to paint them acrylic flat black and then do the metallic gray drybrush thing. Or, you could just paint the pads black and use a wash to darken the silver parts.
One thing about the stock Tamiya tracks is that there is no detail at all on the insides, so what I did when I originally built this kit with the original tracks was to simply draw with a pencil and ruler lines across the insides of the tracks to represent the individual links. After a bit of weathering, the effect was quite convincing, and much better than the original smooth surface.
Good luck, Littlemoe! I hope this has been helpful.
Post some pix if you can!