Dies to Removal

Tezzeret, Agent of Bolas: Yeah... you're not
playing this deck if you're not playing 4 of him. I've seen decklists with 3 copies and never understood why. He's only really bad when you are low on lands and draw multiples. If you have a healthy mana pool and you draw multiples you can chain his -1 ability to create a pretty scary army.

So how do you use him? Generally you would want to build up to his ultimate and use his +1 to dig for stuff to either protect him or mess with your opponent. Abuse his -1 if you are facing an opponent whom you need to clock (e.g. a control deck or slow combo deck) or if you really really need a blocker.

Mana rocks

Dimir Signet
Golgari Signet
Talisman of Dominance
Just play a mix of these. They help you get to bigger spells, allow a lower
land count, and can become 5/5 beaters later on. Try to avoid the 3 CMC rocks like Chromatic Lantern or Coalition Relic. You want to be holding mana up for counterspells or throwing down bigger threats asap, and they don't help you ramp into a turn 3 Tezzeret.

Hate cards

Nihil Spellbomb
Relic of Progenitus
[card]Tormod's Crypt[/card]
Torpor Orb
Ensnaring Bridge
[card]Grafdigger's Cage[/card]
Engineered Explosive
Ratchet Bomb
[card]Executioner's Capsule[/card]
Chalice of the Void
Pithing Needle
Spellskite
Most of these are all-stars in
people's sideboards. The cool thing about this deck is that we can actually maindeck most of them, since we are able to turn them into 5/5s. Moreover, they are generally useful even outside the matchups they were made for, such as Ratchet Bomb being able to answer problem permanents, [card]Grafdigger's Cage[/card] stopping random persist creatures, flashback spells, snapcasters, Spellskite being a 0/4 blocker etc.

Creatures and Finishers

Tidehollow Strix
A necessary evil. Not having Baleful Strix is a bawww for this deck, but this guy is still decent. Serves as an early blocker, can be tutored with Tezzeret, can clock a combo/control opponent etc. Is also a decent topdeck.

Wurmcoil Engine
This guy is our alternate win-con, though he wins the game by himself possibly more
often than Tezzeret's ultimate popping. Difficult to answer; what's more to say about him?

Batterskull
Equip him onto Tidehollow Strix or one of your 5/5s when the germ token is dead.

Inkmoth Nexus
Our singleton out against Tron, Sisters, etc. He turns into a 5/5 flying infect monster when you use Tezz's -1 on him. Other than that he's pretty much a generic mana producer.

Creeping Tar Pit
Desperate times call for desperate measures. Sometimes you just need a 3/2 unblockable. Good stuff to round off your deck's threat density.

Counterspells

Mana Leak
Cryptic Command
These are generally the only counterspells you want to be
playing. They are easily the best in modern, with Mana Leak being the lowest CMC counterspell that has a wide variety of application (as compared to, say, spell pierce), to Cryptic Command being the best high CMC counterspell due to its ability to bounce problem permanents, fog for a turn, or draw you a card. If you want to expand into more counterspells, I would suggest:

Spell Snare
Spell Pierce
The rest of the counterspells like Negate, Steel Sabotage, Dispel etc. are sideboard material.

Removal

Maelstrom Pulse
Abrupt Decay
These cards are the reason why we are going into green. They answer problem permanents which U/B is unable to handle, such as Stony Silence,
Blood Moon, Leyline of Sanctity etc.

Damnation
What is a control deck without a sweeper? No regen means Thrun the Last Troll is not getting back on his feet again.

[card]Executioner's Capsule[/card]
It's a delayed Doom Blade! Playing against creatureless control? Turn it into a 5/5!

Doom Blade
Go for the Throat
Smother
[card]Hero's Downfall[/card]
Dismember
These are all pretty decent. Run some number either in the main or side to round off your removal package.

Discard

Inquisition of Kozilek
This is the premium discard of choice for this deck. It is better than [card]
Thoughtseize[/card] as you don't want to be taking too much damage. It hits a variety of problem permanents and slows combo decks down.

Thoughtseize
Duress
These are ok too if you fancy more discard. I would prefer not to take damage from thoughtseize, though I wouldn't fault anyone for having a number of these in the sideboard to shore up fast combo matchups.

There's not much to say about sideboarding which any experienced modern player would not already know.

Generally, you want to have a variety of answers for different decks. As the maindeck only runs 60 cards, some of the hateful artifacts can be moved to the side instead of being in the main. An example is Chalice of the Void, which can be brought in against stuff like bogles, burn, infect, or living end.

The same goes for
the control package. Cards like Negate are obviously sideboard material, coming in against combo decks like Scapeshift and other control decks.

Just run what you are comfortable with and sideboard accordingly. You can use my sideboard as a good foundation, as I tend to build sideboards for wide-open metas.

One card to note, which I think is crucial in the sideboard is Fulminator Mage. My opinion is that any modern deck running red or black and expects to play any sort of control role at all needs 3-4 of these guys in the side. Aside from obviously helping against Tron, Jund, and UWR, these guys are your go-to sideboard cards against a variety of rogue decks when you have a number of dead cards in your main but nothing to replace them with. At worse, they are 2/2 beaters (still better than holding a damnation against an Ad Nauseum deck). At best, they color-screw your opponent. I play the full set as I
feel that Tron is very, very difficult to beat with this deck.

Like all decks, any matchup is a beatable matchup as long as you draw the right cards. With that said, Tron and Tempo decks like Travis Woo's NinjaBearDelver are pretty rough matchups. Affinity is a bad matchup if they get inkmoth nexus going. Fair decks like Tarmogoyf-based decks or control decks are pretty decent matchups.