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In this particular spot I find KJ of clubs in late position. 2 limp in from early position. I raise it up to 400, hoping to pick up a small pot here preflop (which frequently happened), or to build a pot in position.
First of all, as I usually do suggest when trying to steal with a hand this marginal, raise more pre-flop and try to represent a big PP or AK. With the blinds at 50-100 (150), and with 2 limpers (200), the pot is 350 right there. I'd raise it to 600-800, because I want hands like 109s to get out of the way and think I have a BIG hand. A hand like KJs also has a better chance of winning heads up, especially in position, and raising more can do that.
You also had an early-position limper flat call your raise, and the BB with a big stack do so as well. That screams pocket pairs 22-10's to me first; suited connectors like 109 or QJ also scream out as well (especially from the bigger stack; he's betting 400 from out of position trying to hit a homerun) because they are hands that can thrive in multiway pots 3 or more.
Here is my next suggestion. I don't even want to even say this because I know how much people love to throw tin foil hats on this forum at anything non-conventional about poker and tell each other how much people are wrong. I know I'm gonna get ridiculed for even suggesting it:
Check the flop.
I got this idea from Phil Gordon, who says that sometimes if you are up against C/R, it can be correct to check. The reason why I suggest it here is because if you have this knowledge (as you stated below):
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Surprisingly, the BB check raises and makes it 2500 to go. While it's possible I'm beat here by obvious hands like QJ or 2 pair, I'm thinking this player is beginning to grow tired of my post flop continuation bets and steals, and may be pushing me around.
I'd try to disappoint them and check behind and make them pay for trying to C/R (or C/R bluff). They have a feeling that you as an aggressive player will probably continuation bet 70%-85% on hands raised from late position. And remember, you raised because you tried to steal some blinds and calls pre-flop with a
marginal hand. It's not a hand I'd want to play a big pot with, and neither did you:
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I don't want to get involved in a huge pot here on just the flop
You don't want to get involved with a huge pot with just a pair of Kings, Jack kicker on a dangerous board with 3-way action. With your gutshot straight draw (that might not even be good vs AJ, which players do have a tendency to play weakish) and backdoor flush draw, you have a hand that free cards help, not hurt.
When I check and see a turn, I often think to myself, "What cards help me and what cards make it easier to call a bet of the pot?". If he jams the turn (or if the other player does, like say he had 44 and hit his third 4 on the turn) and bets REALLY big, then you can safely throw away your top pair UNLESS:
If a K comes on the turn, K8-lower and 109 have now become counterfeited, and you have 6 outs versus 10's full of Kings.
If a club comes, you can call a bet on the turn and have outs to the flush, unless it is the 9

, where in that case you might be drawing to a one outer, the Q

, if the villian has quad 9's.
If a J comes on the turn, it's not a great card, but we can still call a bet and boat up on the river if we are beat by a set of 9's or 10's, or a straight.
If an Ace comes on the turn, especially the A

, re-raise and jam all-in UNLESS the other player from EP does so (because he probably has an Ace). The Q

is a good card, too.
With a pair of Kings and a straight flush draw, you can potentially semi-bluff out stronger hands (including a set, which would bet out) that might fold because they might have feared that the free card (like the Qc) that they just gave you, just made a straight with AJ (which is a hand the BB could definitely put you on) and have tons of outs if called by two pair (including the other Aces and Queens which give you a bigger two pair). The Ace is also a great scare card versus 109, who might fear that you have AK.
You can always also induce a stone cold bluff, but I doubt it here because there are too many players in this pot.
Now, I do bet here most of the time.......about 90%. BUT if I am C/R when I do, I feel as if I
have to fold it because I am beat 90% of the time unless I am up against a complete donk.
If a player, especially one with chips, calls a bet out of position, then check-raises me when I just have top pair (especially with NOT top kicker) on a semi-dangerous board.....I have to lay it down unless it is short handed or up against a maniac. Especially such a smallish re-raise of just 1500 (he should have re-bet the pot because his hand is VERY vulnerable, about 3500-4K).
This play can work. I did it once before during a live tournament where I saw a player who would ALWAYS attempt a C/R with his monsters. I once raised from late position with the A

4

. The C/R called from the BB. Flop 6

8

2

. He checks, and I would usually most of the time semi-bluff here, especially against a tight player, but I checked behind. Turn J

. He bet the pot, I jammed, and since he was somewhat pot committed, he called with the 8

8

for a set. He failed to boat up and I won a pot that helped me win the tournament.
What he said after the hand was done, "Man, you are so aggressive, I figured that you would bet out 2 spades there".
And whenever you can do something your opponents wouldn't expect you to do and get there, your opponents make a mistake you can gain from.
Let the ridiculing begin!