Solid axle rebuild question for my Lincoln Town Car

I'm pretty frustrated.  I rebuilt my rear axle with new bearings and seals, installed a new limited slip differential, set the back lash and the gear mesh pattern looks good.  

I've had a heck of a time getting the axle shafts to push in far enough to insert the C clip that retains them. In fact, I inadvertently broke the axle bearing race on the right side and didn't realize it.  Immediately ruined the axle and bearing of course.  So, new axle and bearing and try again.  

So, two questions.  1) why the heck don't the axle shafts move in far enough to easily put the C clip in place? They were a total beast to get off in the first place.  The bearings and seals were driven all the way in, I'm certain. 

2) Should I remove the differential and axle on the opposite side to clean out all the glitter laced oil? Metal shavings have definitely gone everywhere and I don't want to destroy the new bearings on the differential and pinion. What's a good way to clean the axle housing? Spray diesel everywhere and let it dry?

This may sound dumb but have someone push the axle in while you put the c-clip on.  I had a similar problem last time I did the gears on my Mustang.

In reply to Patientzero :

I've been using three C clamps to hold it in.  But then you can't rotate it at the same time and last time that seemed to help. 

What is your new differential?  I think I remembered reading somewhere that you can't use a IRS diff in a solid axle because the IRS isn't made to use C-clips.

Are your axles the right length?  Ford makes more than one size for different housings.  Did you compare them to the old axles?  From my Mustang days I know SN95 axles are quite a bit longer than Fox Mustang axles. 

Is the new limited slip a trac loc? If so measure the clutch packs. Depending on the specs it's rebuilt too getting the c clips on really sucks. We built mine too fords maximum recommended stack thickness and it sucked getting the c clips back in the 8.8

It's an Auburn Performance series differential.  It was tough getting the C clips out even with the stock open diff. The new and old axles are the same length.  I don't know for certain that the new diff is made for the Lincoln, just a 28 spline Ford 8.8". 

Any suggestions on how to clean out the axle housing? How clean does it need to be? I'm thinking about putting some strong magnets on the outside of the pumpkin to help gather some of the metal shavings.  I'll probably only run the first oil for twenty miles then pull the cover and drain the oil and metal shavings. 

A rag soaked in lacquer thinner, pushed down the tube with a broom stick. Refold and do it again, change rags and do it again and again untill clean.

In reply to 44Dwarf :

As a gun owner, that sounds like a great idea.

That's what I've been doing essentially.  I was thinking more like how to clean the pinion bearings without removing them and needing new seals and a new crush sleeve and resetting the bearing preload etc. 

In reply to ebonyandivory :

Sounds as if an axle-sized bore snake needs to be a thing.

Will said:

In reply to ebonyandivory :

Sounds as if an axle-sized bore snake needs to be a thing.

Cannon swab perhaps?