Water Damaged, Smelly Wood= HELP!

[Daniel Porter]

Hello from Dallas, TX yall! 

i just closed my first deal (house hack) and i'm currently putting a little sweat equity into this 1970s house. I've been learning a ton so far, and i'm loving it! So, Started tearing up the pretty nasty carpets, and found some pretty water damaged wood underneath, as well as some pieces that had dry rot (or termintes?!), and some of them that had been poorly replaced and covered up with the carpet. 

I've uploaded some pictures below. be sure to click on them to see the full size. 

my question is this. i'd rather not salvage the wood, and just put laminate over the top of it. so my concern is mostly getting all the bumps out (filling with wood putty and sanding) and getting rid of the smell. The pieces of the subfloor ive seen look fine. 

so will filling the gaps of those new pieces with wood putty be okay? and will sanding and repainting/refinishing the room be enough to eliminate the smell? i'd hate to have it all back together and still have the odor there because i didn't go deep enough into removing it. Looking at painting with nilium or killz, and potentially bleaching the floors. is that even okay?? i've seen some articles saying to test a little area of the floor, and if theres no damage, then go ahead. this would be pre-sanding.