1. Is "Caml Virtual Machine — Instruction set, v1.4" by Xavier Clerc - http://cadmium.x9c.fr/distrib/caml-instructions.pdf up to date? He describes virtual machine of 3.12, while current version is 4.04. According to GitHub logs there were some changes in the VM. Did they touch instruction set?

The definitive list of byte codes understood by the "vanila" CAML virtual machine is in byterun/caml/instruct.h, so one could, in theory compare the two lists side-by-side, if that is what you are asking.
 
2. How are handled operations on floats in bytecode? In MosML, which uses bytecode machine of CamlLight, they added set of instructions FLOATOFINT, SMLNEGFLOAT, SMLADDFLOAT, SMLSUBFLOAT, SMLMULFLOAT, SMLDIVFLOAT, INTOFFLOAT and etc.

They are not handled in the byte code.   They are handled by C code in the run time.  Look around line 340 of bytecomp/bytegen.ml on Github to see how those calls are translated.

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Best,
Женя