Oh man Hoswald, I really feel for you. I keep hearing a lot of the same things in my sitch. Getting mixed messages has been a daily occurrence since my problems started a month and a half ago, and it just drives me up the wall...and leaves me utterly confused about how I'm supposed to act.
My W is also going for a combined MS/PhD right now, granted she's a bit younger than yours, but I know that the stress that it causes for her leaves her unable to really concentrate on dealing with the thoughts and emotions about our relationship...think that could be the case with yours as well? In our case, having W staying with her parents for most of the week then having date nights and occasionally staying at our house has really relaxed her. We don't even really refer to it as a sep., but I guess that's what it is. And then I get the mixed message when we have a nice weekend where she says it feels "fake"...what the %$@& does that mean?!?!?!? So yeah, I hear you on the confusion.
The physical thing is a big issue for us too. Since our sitch started W has not kissed me (or anything more exciting for that matter), but we do hug from time to time. She says that being physical is tough because all the negativity has hurt her attraction for me, which killed me to hear but was something that I could understand. And the thing is, I know that my pursuing and talking just amplified that and pushed her further away. Same thing with saying "I love you", which I haven't heard from her since March 8th at about 11:45PM.
What I've decided to do, and this is a BIG 180 for me since I'm a big talker, is to drop all talk about the marriage until her semester is over, and even then to only talk if she brings it up. Combining that with my GAL stuff is really helping, though it kills me not to see her more often and to talk to her about the things on my mind. It has to be done though, and I know it works because her mood is so much brighter when I'm not constantly asking her where we stand. The hardest thing is that when you do get the positive reactions, you want to go a little further and a little further...but that pushing seems to always cross over into a pursuing kind of behavior, at least for me. We have to know where the line is, and we have to constantly tell ourselves not to cross it but allow our W to make the choice to do that. In both your and my sitch, I think both our W's know how we feel...we have to let the choice be theirs.
All in all though, I'd say keep doing what you're doing man...and be patient. I have to constantly keep telling myself that too, but I've learned from all I've read here and from my DB coach that it is an absolute necessity if we want to get where we want to be.
Keep posting too man, I just switched from being a reader to an active poster, and it's already made a big difference for me.
BITS M: 35 W: 27 T 7.5 years M 5 years No kids My EA: 3/08 Her EA: 1/11, discovered 3/11 (ongoing?) ILYBINILY, D mentioned 3/8/11 W at parents house: 4/16/11