When I split the case on my 73 MX250 to flush out the debris from the mouse nest that evidently did get sucked through the carb, will I need to take everything out of the case like the gear cluster and kick start mechanism?
 
The gearbox will get flush out as well although it didn't have no where near as much going on with it  as did the crankcase. I will remove the crank too and check the bearings of the crank and connecting rod, but I  don't know if it is feasible or practical to try to keep the tranny intact. Otherwise I should have everything else removed that is needed to replace all the seals
 

The "gearbox" and crankcase are 100% separate, nothing is shared between the two internally, so the mouse nest could not have entered into the transmission area unless the fill cap was off. You will only need to clean out the crank side, and as others have mentioned in other posts, if you're only dealing with mouse poop and nest debris (no metal) then you could successfully wash the crankcase out of all that organic debris, especially with compressed air after and save splitting the cases. 

Yup I am aware of that, but can I flush out the case without taking out the gear cluster, with out it becoming a fiasco trying to keep it in the case? In other words, will the cluster try to fall out on its own while moving the case around flushing out the lower end....

PS. There is enough oil film to make all the organics stick to the case pretty good...

Sorry, late to the party here.
From the picture above, looks like the only thing that may give you movement/problem would be the kick starter .
It may stay in place or it could pop out depending on if you grab it or wrestle the motor .
If it does, watch out for that spring, it can and will get ya good.
What are you going to flush it out with?
 

if the trans operates properly and the bottom end is smooth and has no play or noises or rough spots and the mice only set up camp in the crankcase, then I would pop the main seals assuming they are 48 years old, check out the main bearings and flush the crankcase out with BBQ fluid and compressed air and save a massive hassle splitting the cases for nothing assuming trans works.  I would also change the output shaft seal, the clutch release seal, etc. Check the shift pawl that rides the shift drum pins and clutch plates for wear.  How's the bore look?

Was looking at the pic last night & really looks like best to do a complete dismantle & clean to inspect. Mouse family can hide anywhere. This was mine on startup. 

I have a seal kit for the case, everything except for the O ring behind the primary gear. I have access to a parts cleaner, just used it to clean some of my front fork parts and clutch, just to give that an inspection. Glad I did, it was stuck together pretty good. I will need to clean the clutch plates up a bit, nothing rough, just discoloration from the friction plates. Kinda like a light rusty color.

I still see cross hatching in the bore. Safe to assume that the 3rd overbore is a recent overhaul, speaking in terms of hours on the motor? It is easily detectable on over 50% of the bore. An enlarged picture in my first post, allows the cross hatching to be seen in my post.

The transmission does operate smoothly, I haven't shifted it in over 40 years, but it did back then. I did not ride it that long before I put it on mothballs. My concern is now, regarding what looked to be a white residue in the bottom of the transmission, also in an earlier pic, just tonite I ran my finger through it and it felt like it was metal chips in the mix. I set some aside to check with a magnet when I get back in my shop.