Well then drop the crossover further till the mudiness goes away, a floorstander would have been a better solution to your problem, it would have given you the scale as well as better extension in the bass (compared to your bookshelf and not a sub) without the fussiness of a subwoofer (by this I dont mean FS's are a replacemnet for subs). Now that you have a sub, you'll have to keep tinkering little by little with the crossover and gain till you have it to your liking.
The answer was a Floorstander.
Thats ok to where its pointing, pull it out if possible and see if there a reduction in boom without compromising the impact