101Jr Brake seal stud really long???

Hello,
Referencing my previous post about brake seals (http://www.yesterdaystractors.com/cgi-bin/viewit.cgi?bd=mf&th=152214), I've run into a new snag.
One of the left brake driveshaft seal housing studs is much longer than the rest. The lower forward one appears to hook through some component in the transmission.
I've taken a photo, attached, and the good news is that this item doesn't appear to be threaded, BUT (notice, BIG BUT here) it sounded like something went 'tink' when I removed the long stud. I've used a long magnet, and haven't found anything yet, but you know how THAT goes...
Before I reassemble, I'm trying to determine if there is anything else there that might have fallen or can cause damage.

I'm suspecting I probably need to gain access to the top of the transmission, the larger plate aft of the transmission shifter housing.
This tractor has the power lift attachment installed, and unless I'm wrong (please tell me I'm wrong) it appears I have to remove the pto shaft to remove the large plate on top of the transmission.
I am willing to remove the PTO shaft if necessary, and already have the front bearing removed, but am stymied with the rest of the steps to get the bugger out.

Honestly, this project went from a 'quick clean and paint' to a nightmare over the past couple months (actually, since I shattered a piston at idle last year...), and once the brakes are done, I'm hoping to put some paint on this beast and get some wood split!

Any and all advice, encouragement and abuse is welcome...

Brake Seals leaking

OK, well, here's an update with some photos...

First new photo:
I am fortunate to have a brother with a boroscope, and when I peeked below the spot shown in the original photo I saw a nut and washer directly below, so, no doubt something went 'tink'!

So, now, the PTO Shaft. Much easier than anticipated. Pull the 4 bolts off of the PTO shaft housing, then hit the housing 'gently' all around until it starts to slide. Of course, the PTO shaft coupler was not properly installed and fell in, no biggie, but good to get fixed.

Second photo:
Now the Lift Assembly came right out, and I can see what and where I need to.

Last new photo:
Does anyone have any idea HOW the nut/washer are supposed to be installed? I literally have no idea, it could be used as a spacer, or 'torque'??

One last image, I promise.
Attached is the image from the page in the Service Manual, but the graphic is not clear.

It states:
"Remove nut holding pump on stud and back stud out through brake opening far enough to permit removal of pump."

I'm trying to figure if the nut is intended to 'push' the pump gears together, or hold them apart.

It seems important to know which side the nut and washer go on the pump. I'm leaning toward the nut 'pushing' the pump into the gears, as there is no lock-wire on this nut (Between the housing and the pump). If it 'pulled' the pump away from the gears, it might fall off and cause great damage (on the open end of the stud when installed).

Thoughts??