For some reason my rear brake cable is having difficulties with that entry port. Tried different housing lengths, but it seems to end up pinching/crimping or sliding out of the ferrule. I noticed a few pro teams actually run a few Nokon links because of this, but hadn't tried that yet myself. Does anyone have any advice? Its a stupid problem and I'm surprised its giving me any grief at all.

Is the rear furrule stop in place? The ferrule stop is loose and will fall out when un-building or building up. What size is the frame... some smaller frames the rear brake cable routing is quite different.

I believe on the 48-52 evos the rear brake routing exits underneath the top tube instead of the back of the seat tube.

You say "entry" port, so I'm assuming you're talking about the stop at the head tube. That area is always an issue with the EVO. Fortunately, it looks like Jagwire may be coming to the rescue with a housing end cap that incorporates a strain relief. (for those unclear of what that is, It's a tapered, accordion shaped rubber part that supports the housing , allowing gradually more flex as the housing gets further from the stop.)
-It comes in their newest cable sets, the "universal sport brake xl" model. Called "anti kink end caps", their intent is actually for use on folding bikes.

I have a 58

Yah it seems no matter how I trim the housing that it ends up eating the outer housing up at the joint. I'll look for that Jagwire end cap. It doesn't hurt braking, its just really annoying.

I have set up many 58's with no issue. The front will have no ferrule on the housing going into the frame. The rear should have a furrule stop that is loose in the frame very small black piece that just sits in the frame. The cable and housing that comes out of the top tube side will NOT need a ferrule. Hope this helps.