BuildCraft version: Alpha 7.99.15 (MC 1.12.2)
Forge version: 1.12.2-14.23.2.2611
Link to crash report or log: Gist
Singleplayer or multiplayer: SP

Steps to reproduce:

• Build a refinery with two engines (stirling and combustion) one distillery one heat exchanger and a pump with infinite water source. Stirling engine powers the pump and combustion engine, filled with cool fuel, powers the distillery.
• Refine one batch of 16 B of oil (searing), both engines filled up at the start.
• Make a blueprint of the entire thing (including the infinite water source)
• Try to build it in a builder.

Additional information:

If I manage to boot up the world, and prevent it from crashing, I'll post a download link. I'll also try to post a download link for the blueprint file (I assume it's stored alongside the save).
Keep in mind, the world used was superflat with "Redstone Ready" preset.
Also, there were a bunch of logic gates, pulsars and signal wires.

Please update the bc version number in your issue as 7.99 is not a completed version number

Just an FYI:
As shown by the builders recipe being removed in 7.99.15, the builder is not really ready at all, let alone for survival (along with a few other things). The builder currently only 'properly' supports vanilla blocks and and doesn't even support BC blocks themselves so don't expect it to work correctly.

Duplicate of #4076 ?

Ok, managed to fix my world. At a glance, this definitely seems like a duplicate of the issue 4076, but I'd recommend leaving either this one or the other issue open, because closing the issue implies it's been fixed and is working properly now.

Fixing the world meant opening it up in MCEdit, and removing the part where the builder was building a new refinery. Just filling it with air blocks was enough.

Edit:
Considering #4076 is slightly more comprehensive (describes other, less critical issues, that I've also encountered), I recommend reopening that one and closing mine as duplicate.

Ok, I've reopened the other issue.