Unfortunately, so far as I can find, the only advice that any Rogue Trader book offers on the subject of installing cybernetics is in the Attaching Bionics and Implants sidebar on page 152 (at the end of the cybernetics section of the Armoury chapter), reproduced below:
Implants and bionics are only available if the character has access to both the resources and skilled labour to have them installed; commonly this is only available
in substantial medicae facilities and worlds with a very high technological base.
If a character can find a doctor willing to install a bionic or implant then the process takes no less than 2d10 days, minus one day for each point of his Toughness Bonus—to a minimum of one day. How difficult it is to attach a bionic or implant is up to the
GM. He may decide that given enough time, and in an advanced enough facility, it is automatic, or he may call on the doctor to make a series of Medicae or even Tech-Use Tests that could lead to such things as permanent crippling or Blood Loss (see Chapter IX: Playing the Game, page 260).
As you can see, it's far from a fully fleshed-out mechanical system and explicitly leaves deciding on the details up to you, the GM. However, it does offer us some important information about how challenging the installation process is meant to be to inform that decision; and, where the GM judges that success is not automatic, essentially suggests making an extended test using Medicae/Tech-Use skills, where failure may have drastic consequences for the unfortunate subject.
I'm not going to come up with an entire mechanical system for you - that's beyond the scope of what we do on this stack - but I will make a few observations for you to keep in mind when you come to adjudicate how this works:
- Cybernetic surgery requires advanced medical resources that are not commonplace, usually found only in "substantial medicae facilities" or on relatively very technologically advanced worlds. A Rogue Trader's vessel undoubtedly has decent medical facilities (as well as the facilities to maintain its complement of servitors), so attempting cybernetic surgery on board the ship is probably possible, but success should not be automatic, and probably any tests made in such an endeavour should be at least Difficult or even Hard to reflect the lack of specialised equipment.
- Cybernetic surgery requires highly skilled professionals who are again relatively rare. Besides obviously requiring training in both Medicae and Tech-Use, you may wish to also require that the character attempting surgery has the Master Chirurgeon talent, to represent advanced surgical training. (The Explorator does not gain access to this talent until Rank 7, which might move such self-modification a long way down the path of character progression - the majority of the Adeptus Mechanicus don't do their cybernetics themselves.)
- Cybernetic surgery has the potential for drastic consequences if it goes wrong. The text suggests loss of limb functionality or even Blood Loss as consequences if the surgeon fails their tests. I'd be inclined to suggest referring to the Critical Damage tables for Rending damage in appropriate locations for possible consequences of a surgical failure, or even Energy damage depending on the nature of cybernetic being installed; you could perhaps inflict the degree of failure on an unsuccessful test as Critical Damage to the subject (it's more forgiving if the test doesn't fail by much, and ties it in to the existing damage system so you already have mechanics to use for consequences and recovery if things go wrong).