For a subwoofer I think your choice was just fine since you probably wouldn't ever notice any resonance if there was any. As for your situation with the glue sealing the pores, if you can't get all the glue with water then I usually take a little sand paper to it after it dries. The yellow glues will generally sand off pretty easily since they harden well. You can also take a scraper to it which works well too. Another thing is taking a wet towel to the dry glue and an iron. You can iron the wet towel over the glue and it will re-activate it to a small degree, then you can usually add more yellow glue to that and it will bond well. If it was just a little glue slop here and there then I wouldn't worry about it at all, I'd just be sure it was sanded flat and glue it up. Don't use clamping pressure to compensate for a poor joint, MDF is cheap, make another panel if your cut is less than acceptable. Clamping harder to squeeze a bad joint together starves the joint of glue setting you up for a joint failure in the future. Don't get hung up with fancy jointwork. Simple butt joints with yellow glue will be very strong. Rabbet joints for braces are a good "upgrade" if you are feeling up to it, otherwise the simple butt joint that fits properly is more than enough. Keep it simple and take your time! Hope it helps a few people.
but you now have an excuse to acquire more TOOLS! The only thing I enjoy as much or maybe even more than woodworking is acquiring new tools. The satisfaction is great too isn't it? If you find you really enjoy the woodworking part of it you should definately invest in a good contractor style table saw. You'd be amazed at the quality you can achieve. It might be a bit of overkill though if you don't intend to do much woodworking. 
