(Part 2) Top products from r/whatsthatbook

I know this! This is one of the fictional journals from the My Name is America series, The Journal of Patrick Seamus Flaherty. I am super impressed you were able to remember that much about it.

As a bit of extra bonus knowledge, his sister also has a journal from the same time period in the girl's Dear America series.

I answered this over at /r/tipofmytongue as well -

It might be Dead Water Zone, by Kenneth Oppel

>A well-realized world of rotting docks and ramshackle buildings on the shore of a polluted lake forms the setting for this haunting character study. Summoned by his brilliant but frail brother Sam, Paul leaves his comfortable suburban neighborhood for unsavory Watertown--and finds that both he and his brother are being hunted by the quasi-legal Cityweb: Sam has discovered a mutated microorganism in the lake that, though eventually toxic, greatly enhances physical ability. But despite plenty of danger, narrow scrapes, and a lurid, violent climax, outward events seem almost incidental compared to Paul's inner struggles. Once complacent in his role as protective older brother, he's angry to see Sam growing up and away from him and racked by guilt to feel so; his turmoil increases when he meets a new Sam--preternaturally fast and strong, exultantly freed from his former metabolic disorder. Oppel explores the brothers' dependent love-hate relationship with some sensitivity, though the confessional tone gets heavy at times. Glamorous but deadly, the microorganism is like a drug, so the story can be read on that level, too; indeed, Oppel adds a subplot involving a streetwise young Watertowner searching for her lake water-addicted mother. A thoughtful story with an unusual combination of ingredients

Sounds like Ready Player One by Ernest Cline.

http://www.amazon.com/Ready-Player-One-A-Novel/dp/0307887448

Number 2 sounds like this My America book.

Sounds vaguely like David Macula'y's "The Wat Things Work"
http://www.amazon.com/gp/aw/d/0395428572?
pc_redir=1395279960&robot_redir=1

Can you give an approximate year of when you read this series?

Your description reminds me of Doomsday by John Peel.

It was! It was A Big Ball of String.

Would it be Shade's Children by Garth Nix?

I vividly remember the part about the kids getting paired off each night. I think the goal was to repopulate the movement or something?

It's not The Way Things Work, is it?

The Roar by Emma Clayton?

Raven's Gate?

The Last Book In The Universe by Rodman Philbrick?

https://www.amazon.com/Last-Book-Universe-Rodman-Philbrick/dp/0439087597

The Last Book in the Universe?

The Tremaris trilogy? https://www.amazon.com/Chanters-Tremaris-Singer-Songs-Trilogy/dp/0439554799

The Chanters of Tremaris?

The Westing Game?

Seedfolks is about a vacant lot that begins with a young girl planting some beans and turns into a community garden through other residents perspectives.

Seedfolks? https://www.amazon.com/dp/0064472078/ref=cm_sw_r_cp_apa_i_usS3DbBP2NPSB

Singularity by William Sleator?

http://www.amazon.com/Earthquake-Terror-Puffin-Novel-Kehret/dp/0140383433

I've read this before. Sounds similar but it has been a while since I read it.

The Final Journey?

Deepwater Black maybe?

https://www.amazon.com/Westing-Game-Puffin-Modern-Classics/dp/014240120X
The Westing Game (Puffin Modern Classics): Ellen Raskin ...

Journey to the River Sea fits some of those details.

Ready Player One?

Bonechiller by Graham McNamee? The female character Ash doesn't seem to be in the military and online descriptions don't go into the monster's weaknesses.

Is it Dead Water Zone by Kenneth Oppel?

https://www.amazon.com/Dead-Water-Zone-Kenneth-Oppel/dp/0316651028