I had the same problem with one of my BLI F3's, and it was the big blue Rolling Thunder antenna wire on top of the decoder that was the problem. The speaker wires are tiny so they weren't interfering with anything.
I just repositioned the big, thick blue Rolling Thunder antenna wire, and the shell easily fit lower where it should be.
I have an ABBA setup (UP of course) so there is no Trainphone antenna things sticking down through the shells on my stuff.
Since in my time period UP still had doors on the lead unit's pilot coupler, I removed the coupler on my lead unit and put closed coupler doors on, which were included as accessories in the jewel case, which just happened to make shell removal much easier on the problem A unit. I used MTL True Scale couplers to replace the supplied couplers and an N-Possible on the nose of the last trailing A unit. When I get around to it, I'll replace all of the couplers with N-possibles, but, this lashup is what I run on my layout with no switching duties, although I've been tempted to throw a GP-9 into it to ugly-fy it as UP was infamous for. Luckily, N-Possibles couple up to Tru Scales, so no problemo.
Since I'll never be using BLI Rolling Thunder, I considered just snipping the antenna off...or de-soldering it, but, repositioning it worked out fine, so I kept it attached.
Cheerio!
Bob Gilmore