LOL, "dirt cheap" and "custom MKIV break swap".... Have some details for us? We might have to make these guys famous.
You may have some issues with the ABS system but I don't know how bad any symptoms would really be. The front wheels are still monitored independently, the rears are monitored as a unit and the computer is still in place to ensure that they keep rolling as needed. All that I can imagine is that the system might function too aggressively.
I would be more concerned about making absolutely sure that all 4 wheels are upgraded properly to maintain the appropriate bias... Trying to leave the rears stock and screwing with proportioning valves isn't going to cut it.
Personally, I'd install some braided brake lines, upgrade the brake fluid and install a larger 4Runner master cylinder and see how that feels for a while. You may need the 4Runner master cylinder with the MKIV calipers anyway.
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