That's a hell of a story. I'm sorry to hear about the clutch giving you fits. I'm not one to shit on shops or dealerships openly, because sometimes things can be lost in translation, however what you've been told doesn't seem correct in any sense at all.
First of all, the suggestion that you need new engine cases because a bearing is bad is idiotic. If the bearing is bad, change the bearing, that's why they can be pressed in and out. Secondly, if you had bad radial run out on the primary drive/clutch drive bearing, you'd probably have ruined the oil seal and noticed a leak after riding on it like this for multiple years. Either way, you can easily replace the bearing if need be. I'd wager that bearing being bad couldn't cause the symptoms you describe anyway. Moving along.
So let's get this figured out the proper way before we're buying engines on some guy's suggestion who sounds like he knows not what the fuck he's doing.
Symptoms - What you described of the faulty clutch master cylinder sounds plausible, I've seen it many times. The master cylinder internal valve does not allow the pressure to be released back into the reservoir. This causing too much 'resting pressure' in the clutch hydraulics and makes the clutch slip or hydraulic fluid start to leak. Replacing the master cylinder was the right call.
If you're now having an issue where the bike is creeping forward even with the clutch lever pulled completely in, you have one of the following problems:
1: The clutch hydraulics have not been bled properly, so when you pull in the lever, you actually compressing air in the system which prevents the pressure plate from being properly pushed off of the clutch discs. This is why the bike continues to creep forward in gear even with the clutch pulled in. Bleed the clutch hydraulics again. A genuine brembo master cylinder should have a bleed valve on it.
2: The slave cylinder is failing and allowing air into the system when you pull and release the clutch lever. This ultimately causes the same symptoms as #1. Bleed the clutch.
3: The new clutch master cylinder piston isn't adjusted properly meaning when you pull the lever you're not actually getting the proper amount of throw on the piston. This results in the piston only moving a little bit, and BARELY lifting the pressure plate off the clutch discs, but still not enough to let the bike roll easily with the clutch lever pulled in. If you bought a genuine brembo unit, this is very unlikely. Go back to problems 1 and 2.
4. Get the manual for the clutch, stack the plates according to the manual. The only way the clutch is causing drag is if the stack height is WAY too tall. This is almost impossible unless you've started adding plates that didn't come with the clutch. But I know how it goes when you're chasing problems and 'trying anything and everything', so put it back to how the book says it should be. Let's not create new problems trying to fix old ones.
Before we get into the whole bearing possibly being or not being bad, let's get the clutch sorted first. Once you've done ALL of the above report back with your findings and let's get this thing fixed. I promise you don't need an engine.