When decompiling, make sure you have Java 8 or Java 7 (Preferably 8) in your PATH (or equivalent). If not, MCP will start trying to use whatever Java it manages to find, which is REALLY bad.
See above.
If you recompiled with Java 9 or above, when reobfuscating, SpecialSource with error out with "unsupported major class version". This means MCP went ahead and used whatever Java install it could.