I used to have a huge system like that in mine about 15 years ago. I understand the need to tone it down, but not lose all the fun out of having a great system. This is just what I did (take it like a grain of salt), but I would remove the whole box. It looks like you are using 6.5" round and 6x9's oval with maybe 2 12" subs. Did I get that right?
I changed the 3.5 stock tweeters to the small 1" domes (will have to build a bracket to fit), with 6.5 door speakers, and then the 6x9's in the rear. The only way you are going to get the same sound is to run two amps a 6-channel for the 6 speaker system, and a mono amp for the 2 subs. I was able to reduce the 2 Sony 12" subs to just one Rockford Fosgate P series as they are that much better.
This will save a crap load of room and give you the ability to put the cage in. I have the same plan as you to run a MM 4-point cage with the low slung bars option in mine.