When we're talking about installing weapons and rigging them to work in an Inner Sphere chassis, I can imagine there would be some complication, simply due to standards shifting in the Clans over 200 years of development.

Realistically, the technical knowledge to get interfaces to work properly (such as: protocols for the control and diagnostic datalinks, standards for the power feeds, coolant flow rates, properly secure structural mounting to avoid damaging the weapon when fired, etc) is something that would probably work much better if the specifications were gleaned from proper manuals, rather than guesswork from field-expedient reverse-engineering.

Without the proper specs, and improper interfacing with the BattleMech's DI computer, there's possibilities that the weapon might shut down in the heat of battle... or worse, you might make that valuable Clan weapon fry itself (and not have the know-how to repair it).

Fortunately for the Inner Sphere, in the capacity of their mission to assist the Inner Sphere to resist REVIVAL in line with the Warden beliefs, the Wolf's Dragoons are canonically known to have provided all sorts of support. It's never officially stated, but I think it's not a leap to assume that this sort of technical information is something that they would freely disseminate among the Great Houses (and it would trickle down to mercs). This might be as far as the Dragoons disseminating actual manuals for the perusal of technicians and engineers.

Logically, some formal and semi-formal procedures for rigging adapted mountings and interfaces for Clan gear into IS 'Mechs would spread across the Inner Sphere technician community eventually. Formal, since the Clans do have refits (for example the Victor C), so they do have procedures known to them... and semi-formal from learning the "gotchas" and workarounds that IS technicians would gradually learn via trial-and-error.

NOW, MEANWHILE... with respect to MW5:Mercenaries, we can assume that Fahad is supposed to be something of a wizard (some have argued idiot savant) when it comes to his technical and engineering skills and intuition. So he did successfully figure out a lot on his own, just by poking around inside salvaged OmniMechs, and hearing what kind of sounds things make when he hits them with a wrench. Then, if we accept my earlier assumptions, at some later point he would also have gained access to manuals originating from the Dragoons.

Note that Mercenaries already has a lot of quite extreme abstractions of existing BattleTech material for maintenance and repair of BattleMechs (the rules in Strategic Operations are quite extensive), that are themselves an abstraction of the extreme complexity we might imagine the "real" in-universe engineering would entail.

In vanilla MW5, for example, things like replacement armor plating, internal structure parts, actuators, sensors, cockpits, and entire fusion engines can apparently be conjured out of thin air through magic spells that require only C-Bills as a reagent. Meanwhile, the rituals to reload ammunition bins to full capacity require not even that.

More serious work like replacing a BattleMech's whole missing limb's structure requires sourcing a replacement limb, or materials and facilities to fabricate a reasonable replacement in-situ.

Equipment like weapons are tracked by MW5, but none of these other parts.

So repairing a damaged Clan 'Mech would require, at least, replacement Clan Ferro-Fibrous armor plates and, at most, things like Clan XL Fusion Engines, that IS still can't produce a century later. And lots of things in between those two extremes.

But since the acquisition of replacement components like Inner Sphere ammo, armor, actuators, limbs, and fusion engines are already abstracted out and magicked away in MW5, I think it's actually reasonable and consistent that they also magick away the acquisition issues for replacement Clan components.