Recently, when trying to intonate the Floyd Rose on my E-AL-128, I got the low E and G string VERY close to in tune.. and the locking screws on the bridge were sticking out beyond the routing, making them hit the body when I pulled up. I was wondering if it would be advisable to replace the screws with these...
The ones for the Schaller/Floyd Rose II models.

Now, there was one other problem with this, and that was that the E and G strings ended up being higher than the other strings when I had them intonated, because the saddle was moved so far back on the bridge that it was starting to slide up towards the fine tuners. does anybody know why this might be?
Then there's this band called Slice The Cake...

Bunch of faggots putting random riffs together and calling it "progressive" deathcore.
Stupid name.
Probably picked "for teh lulz"

Mod in UG's Official Gain Whores
Wow, that sounds pretty ****ty, really. Seems like you got a lemon. There should be plenty of room to intonate rearwards on a FR-equipped guitar. The Schaller screws would solve your first issue, but the second would only be remedied by *gasp* grinding down the rear of your saddle/clamp, or raising the others equally with shims and then lowering the whole thing via the studs.

Edit: At least, that's how I see it.