There are several things that could explain what you're hearing.
Before I get into that, you need to be realistic about what kind of bass you'll ultimately get out of those speakers. That's a fairly unusual driver combo; very high end ($400 each) tweeters combined with 4.75 inch midranges. The midranges are always going to be the limiting factor here. The Excels are good drivers, but even with aggressive porting, you won't get a large amount of deep bass out of 4.75 inch drivers. Also, judging from the sensitivity numbers and the other comments on the Wilmslow Audio website, your speakers have no baffle step compensation, which means they *must* be used against a wall or you'll get the impression of lacking bass. That also means that if you make minor changes to the positioning of the speakers, which you probably did when you made the changes to the tweeters and crossovers, you can make a significant impact on the amount of bass they generate in-room. Different positioning alone may explain your results.
The tweeter you moved from (S2905) is quite different from the tweeter you moved to (S2904/7000). The tweeter you had before is actually a little flatter in the top octave, but it cannot be crossed as low. It's possible that the new crossover is crossed slightly lower, moving the Excel driver out of an area where its distortion increases, causing the overall sound of the speaker to become subjectively more bassy, even if its on-axis frequency response is similar. Third harmonic distortion and higher tends to make a speaker sound tipped up towards the upper midrange and highs, giving the impression of less bass. It's also very possible that the S2904 has less total distortion, again causing the same perceptual effect.
One thing is almost certain, the actual amount of bass generated by the speakers didn't change, unless you somehow removed obstacles (e.g. stuffing) from the path between the woofer and the port when you were changing the crossover board. It's either the speaker positioning or a perceptual effect, unless the new crossover adds some baffle step compensation (unlikely).