Hmm...first, a 'try this' thing if you haven't already: the rear wheel (or at least the drive sprocket) needs to be rotating when the engine is not, if you want to attempt a 'manual' shift (so to speak...). This is because of the dogs-and-slots arrangement of the typical constant-mesh gearbox (all of them, not just this one). The gears that are disengaging (like when going into Neutral) will be fine, but the dogs of the next gear will not be lined up for the shift, on purpose, by design. That's why these 'clunk' like they do when entering the next gear: the dogs forcibly accelerate the new gear to the present gear's speed.
I have had just one of these engines go together (in a hurry, and in the dark on my patio one night) when the "C" shift fork did not drop into the slot of the mainshaft where is was supposed to while the engine was upside-down, and the result was a bike that would shift fine into 1st, and maybe into 2nd, but that was all. After that there were no more gears as the drum wouldn't turn until the 3rd gear would slide into the 2nd for the 2-3 shift. I was able to [just barely] see the error by looking up into the (dripping on my face..
) oil pan's opening, from under the bike, and knew I had to pull the engine out just to pull the cases apart, align the "C" fork correctly (the next time I did it at high noon...) and re-drop the bottom case onto the top case...again...and then put all those other pieces back on... And about the other noises coming from below: if the 2nd gear's dogs are TRYING to engage with C5 because of the loading of the "C" shift fork resting against it, this will make the whole gearbox "jitter", which means all those other unloaded gears are rattling their dogs and slots together because they are not being orchestrated by the "C" fork dampening their minor movements.
The only part of this story that aligns with your engine is the "looking up into the (dripping on my face..
) oil pan's opening, from under the bike", but this means once again taking off that Sump Thing to do it (and probably another gasket set?). A word of advice if you then have to [re]pull the engine out to fix this situation: put the bottom oil pan onto the bottom of the engine after removing the Sump Thing's raised housing. It is EXTREMELY easy to dent the bottom oil pan surface while removing/installing this 200+ pound engine, and the dented pan surface will forever leak oil. (Don't ask how I know this, because I won't tell you!
).
