Make sure you put a little bit of RTV on the shaft splines before re-installing the flange, then I like to fill that small cavity area that is left right at the end of the splines and the flange inner splines (hope this makes sense) with RTV, use the little nozzle thingy that comes with the tube. Smear a light coat of RTV on the back of the big washer, put it on the shaft, then a new stake nut. A lot of times these leaks are actually lube coming up thru the splines, not coming around the seal.
As for the "chunks", I would get as much out as possible, maybe with a dental pick and a slim pair of tweezers. Dump a jug of gear lube in the case before you replace the seal so it will wash as much as possible out forward. Then as long as the chunks are just rubber I wouldn't worry about it. Tearing apart that case just to get that stuff out would be a big project, that front shaft and bearing are pressed in. The gears in that case are pretty darned big, nothing wimpy about it. I can't imagine that some bits of rubber are gonna cause any damage.
But if your tcase grenades next week because of crap inside, I'll deny ever writing this, this post will self-destruct.