Connecting an 80's style computer cassette to an FPGA
Decoupling capacitors are known in circuits' power supplies, where they serve to keep the supply voltage clean of (high frequency) noise. But I have the impression that here removing DC content of your signal is meant, by means of a series capacitor, like C24 does for the input. Which, depending on your point of view (DC or AC) can be called a coupling capacitor. But there's no capacitor that does this on your output. The value of C23 is also suspectively low. The cutoff frequency with resistors R23 and R24 is 12 kHz, which is useless, because that will be about the frequency range of the cassette anyway. I'd rather expect 5 kHz here. Also the text speaks of the MIC input, but for that the output level is too high. The schematic mentions the line input.  
The CA3140 is no good. Its minimum operating voltage is 4 V, and at 5 V the output high doesn't go higher than 3 V, so for 4 V supply that may be as low as 2 V, and that may not be enough for the Spartan. Use a Rail-To-Rail opamp instead, or even better a comparator.


edit re your new questions  


Polarity is OK, since it doesn't matter :-). You have an AC signal going above and below ground. Like you've drawn it the positive half cycles will make the output go to Vcc, the negative to ground. If you switch the inputs you'll have the reverse, but both signals will look the same.
Yes.  
I would ignore it. It doesn't seem to have a function other than loading the output, and besides, if you dot it out you're asking for being ignored :-).


Important thing about R1: this should go to Vcc, your 3.3 V, not in series with the output. The open-drain output means that there's only a FET switching the output to ground, so it can only make it low, not high. The pull-up resistor will make the output high when the FET is off.