The issue is I removed everything from it and now if I have it enabled the 4000 won't boot. If I disable the FlashRom it boots fine. From what I have read, I think I need to put the Amiga ROM on it or something like that.
So far I have put the BPPCFix, NoIDE, PsdStackLoader with the poseidon.library and associated usb modules. What I do not know how to do is load the kickstart rom.
Not putting a kick rom into the flash won't cause a lock of the system. First I'd like to know if you're disabling the flash with the ROM-OFF jumper or rather by using the software mechanism (LMB, MMB or whatever you set in Luciferin for the bootloader). If you used the ROM-OFF jumper, try the soft method instead. If it then boots, it is easy to isolate the offending module by selectively reflashing the contents with modules enabled/disabled (flashing is very quick if you only change the type e.g. to Data and don't change the contents or the order).
To flash a whole kickstart rom, you need to add the AlgorKick module and a 512KB kickstart rom file (any name). You can assemble a custom kickstart (e.g. with the boing bag upgrades and rom fixes integrated) using Doobreys RomSplit and Remus tools.