FWIW, I was running 17/14 over these hands. I'd given up on some ugly boards when getting played back at.

1. Villain had called and taken me off of hands several times previously. He was running 19/16 over the 150 hands we played, and I'm entirely sure that the difference was hands that he called my pfr having position on me. Postflop, there'd been a number of spots where I hadn't had anything and had played a few different lines. My thinking here is that he is likely playing back with a wide range. Here I was confident I was ahead on the flop, felt like I was reasonably strong against his range on the turn, but that if I raise every hand I beat goes away. I also felt the FD gave me more hands I could rep (i.e. suited overs). On the river, I decided to mix the equity I felt like I still had with the FE of repping the turned FD. So was the river play just spew?
Full Tilt No-Limit Hold'em, $4 BB (6 handed) Hand History Converter Tool from FlopTurnRiver.com (Format: FlopTurnRiver)

SB ($297.90)
BB ($476.45)
UTG ($181.20)
Hero ($480)
CO ($614.10)
Button ($691.60)

Preflop: Hero is MP with 9, 9.
1 fold, Hero raises to $14, CO calls $14, 3 folds.

Flop: ($34) 3, 6, 4 (2 players)
Hero bets $24, CO calls $24.

Turn: ($82) 5 (2 players)
Hero checks, CO bets $60, Hero calls $60.

River: ($202) K (2 players)
Hero checks, CO bets $132, Hero raises to $376, CO calls $244.

Final Pot: $954


2. An example of the above, though he has to have a pretty decent ace here, right? Here I definitely should have just let it go, but the EP player was just such a donk - I was confident he was going away if pressured.

Full Tilt No-Limit Hold'em, $4 BB (6 handed) Hand History Converter Tool from FlopTurnRiver.com (Format: FlopTurnRiver Cards)

SB ($171.15)
BB ($950.20)
UTG ($313.70)
Hero ($394)
CO ($1148.50)
Button ($435)

Preflop: Hero is MP with J, J.
UTG calls $4, Hero raises to $18, CO calls $18, 1 fold, SB calls $16, 1 fold, UTG calls $14.

Flop: ($76) 4, A, 4 (4 players)
SB bets $20, UTG folds, Hero raises to $65, CO raises to $180, SB folds, Hero folds.

Final Pot: $226



3. Flop was standard against a 54/25, right? On the turn, I expected he could get away from a lot more hands than he could on the river and thought the pot was already big enough for a push to be reasonable on the river.

Full Tilt No-Limit Hold'em, $4 BB (4 handed) Hand History Converter Tool from FlopTurnRiver.com (Format: FlopTurnRiver Cards)

SB ($910.85)
BB ($308)
UTG ($340.40)
Hero ($394)

Preflop: Hero is Button with J, T.
1 fold, Hero raises to $14, SB calls $12, 1 fold.

Flop: ($32) J, K, Q (2 players)
SB checks, Hero bets $25, SB raises to $50, Hero raises to $173, SB calls $98.

Turn: ($353) A (2 players)
SB checks, Hero checks.

River: ($353) 4 (2 players)
SB bets $748.85 (All-In), Hero calls $232 (All-In).

Final Pot: $817



4. Is raising the turn better for extraction? Is the river bet spew?
Full Tilt No-Limit Hold'em, $4 BB (6 handed) Hand History Converter Tool from FlopTurnRiver.com (Format: FlopTurnRiver Cards)

SB ($508.40)
BB ($466.60)
UTG ($400)
MP ($139.80)
Hero ($417)
Button ($369)

Preflop: Hero is CO with 5, 5.
1 fold, MP calls $4, Hero raises to $18, 1 fold, SB calls $16, 1 fold, MP folds.

Flop: ($44) 9, 9, 5 (2 players)
SB checks, Hero bets $32, SB calls $32.

Turn: ($108) 2 (2 players)
SB bets $68, Hero calls $68.

River: ($244) 2 (2 players)
SB checks, Hero bets $100, SB folds.

Final Pot: $244