Measure the voltage at the output of the relays when they are off. <- Scratch that, just found out you did.
I can guarantee that it is not the timing solenoid.
Here are two and a half senarios.
My old 93 with a diesel, setup with electric manual shifting. Logic as follows;
0-Off
1-On
Gear, S1, S2, ST, SL
P -> 0, 0, 0, 0
R-> 0, 0, 0, 0
N-> 0, 0, 0, 0
D-> 0, 0, 0, 0 <- OD ON
D-> 0, 1, 0, 0 <- OD OFF
2-> 1, 1, 0, 0
1-> 1, 0, 0, 0
SL is controlled manually via an external switch, and ST has never been hooked up. This has worked for almost 10 years
Now to complicate things. I rigged up some LED's to each solenoid, though I was recording the patterns as driving but managed to only take a picture...
Vechicle stopped
Gear, S1, S2, ST, SL
P-> 1, 1, 0, 0
R-> 0, 1, 0, 0
N-> 0, 1, 0, 0
D-> 1, 0, 0, 0
2-> 1, 0, 0, 0
1-> 1, 0, 0, 0
This surprised me some, but it works.
Now while driving SL will come on before a shift til after the shift completes. Only from 1->2, 2->3, 3->4, 4->3, 3->2. The on time is different and seems to be slightly dependent on gear change and throttle position. This is from slight acceleration to WOT acceleration. Shift point didn't really follow any of the timing, just while SL was energized.
For funsies I pulled the pin for SL, stuck a resistor across the pin to ground and drove. Basically tricking the TCM and disabling SL, basically it shifted the same. Maybe slightly quicker and firmer but had to really 'feel' it.
I'll try to find my logger, if not will build another for some more data in the next couple of weeks.