Just a quick question...

My group has an operator obviously with a MIU installed as standard, however, he has 'acquired' a good quality version. Should he follow the normal rules for installing this better version i.e. 2d10 - toughness bonus or should it be a relatively easy 'operation'? He does have access to a Mech Priest, facilities and Medic (currently.)

Well if he got it as requisition then the tech-priests would automatically set it in with a surgery.

As for if he should test toughness, then That in my mind depends heavily on the quality of the facility. If its a good facility, then I would wager no. But if its a field hospital on the front line, then he needs to roll toughness.

If the facilities and medic are good, I would rule it as a bonus to TB or a reduction on the dice roll. You could also create a standing rule that replacing any augmetic with a better quality rolls only a single d10 for acclimation.

It would all depend on the circumstances and the game your running.

To start, if the player acquired it through requisition and your playing a fast paced game, I'd make it easy and either have it be that it's a "Plug and Play" and he's done and back in the action, or he's only down for a short time determined by the GM.
If he acquired it through requisition but it's a more serious game, then no. I would say follow JupiterExile's suggestion and make it only be a 1d10 roll rather than the usual 2d10 roll (There just installing a higher quality system of the same type, not something completely different.)

However, if he "acquired" it through other means, I would probably follow the above for a more serious game, plus tack on finding someone to do it for him, unless he wants the Mechanicus to know that he acquired something he shouldn't have. Finding someone to do this could easily be a little subplot for the group to do (assuming that the other members are on board with the idea,) be a good way to have a game even if your short on time.

Whether or not the recovery time is shortened would be dependent on the skills of the installer plus the facilities.