"I wonder if there is software that can help you see how textures align."

Any familiarity with Blender? While I don't use it I know that it allows you to paint directly on the model across seams, thus you can avoid the headaches of the traditional method of lining up or blending textures. Carrara, Blacksmith3d, BodyPaint3d, Modo, etc... all have Poly Painting. Blender is free of course. I imagine that with some knowhow you can generate some painted texture maps rather easily for the Freak. I've used Carrara's poly painting functions on models intended for Poser and the results were pretty nice and pain free, in particular with pre-uv'd models.

Are you using SnowSultan's seam guides for M3/freak? It's the same mesh and UV's so either will do. might help you with your problem.

http://www.snowsultan.com/3.html

"The old M3 texture mapping alignment is very strange."

I don't have M4 (I do have V4 of course, one Gen 4 figure is enough of a financial hardship thank-you-very-much) for male figures I use M3, the Freak (original), and Apollo Maximus... From what I gather though, many texture creators prefer the Gen 3 mapping over Gen 4 as the limbs are part of the body map.