Yes. Had the same issue. It can be overcome, however, if you are willing to let your stock airbox go, because, as you know, it just doesn't line up correctly. This is what I did....
1. The bracket....I had the issue with it interfering with the strut tower. I did find, though, if you were able to mount the bracket about 3/4" forward by using longer bolts and a couple of spacers, it fit just fine. It pulled the intake tube at such an angle that there is now about a 1/4" space between the strut tower and the intake tube.
2. The airbox....Unfortunately, it's got to go. It mounts the assembly at such an angle it just won't line up, otherwise. I got some sheet aluminum and some automotive weatherstripping and made my own, "trick" airbox. I've seen others use plexiglass ones on other cars. You will need some form of airbox to protect your new MAF from the dreaded "fanwash"/resonance issues which has been known to create some quirky idle problems. I ran without an airbox for a little while and had a really unstable idle....after the box, it ran quite smoothly.
3. The air filter....Another issue. Most
K&N-like air filters are made for stock 5-ohs, with a 53mm outlet. You now have a 76mm MAF. Now, this may sound like a "hack-job", but it works....I went to Home Depot and got a white PVC connector that fits over the MAF. I think its an end-to-end connector for 4" pipe. Bring your MAF with you to make sure. It's about 5" long. It JUST about fits over the MAF, but not quite. I used a rotary grinder to shave off what I needed off of the PVC pipe, then it would fit over the MAF snuggly. Then, I took a razorblade knife and cut the correct sized opening on my air filter. I made sure that everything fit rather tight, so it would be less likely to vibrate off.
Anderson Ford Motorsport carries a line of air filters with wider openings that you may be able to use. Doesn't hurt to give them a call.
Perhaps someone else has a better idea, but this works for me.