So I'm currently running one Mesa Boogie Dual Rectifier and one JCM-800 (half stacks) at the same time using a Radial Bigshot ABY pedal. I love the sound of the two combined but they definitely sound like two separate amps playing when played at the same time. It's almost like there's a slight delay or something that's keeping it from sounding like a wall of sound (hopefully that makes sense). I don't think it's an EQ issue so I'm thinking it's the ABY pedal. Anyone here have any ideas of how I can make it sound like a wall of sound? Or another good ABY pedal?

Thanks in advance!!
If you've tried the 180 switch and the iso switch, it's not the A/B/Y. There's basically nothing in the circuit, it's just routing the signal. So unless the pedal is broken in some weird way there's no reason to suspect the pedal.

I would imagine this is a mids issue, where one amp is much more scooped/aggressive than the other and so it's too easy to distinguish the two. I would try going back and forth dialing in and out the mids on each amp to see how they blend. You can also try dialing the treble back and the bass up until the amps mesh a bit better. Sometimes you can do that just from the tone knob on your guitar.
It you might be hearing the sag of Rectifier. Have you tried switching it to diode rather than tube and setting it to bold instead of spongy?