Hello again,
We make I nice team: I did this as a physicist without much idea of the control engineering applications. Only it was some time ago. And no, it is Introductory level.
Because of the elaborate rack/pinion drawing I kind of skipped the interpretation of N
1,2,3,4, the gearbox, but it's clear to me now. so the D
2 is clear also. And it counteracts T(t) in the time domain.
You did a lot of work and I would need some time to read through. Point is, we seem to speak different languages. I, for one, out of necessity have to start in the time domain and then transform. Preferably step by step, to combine steps later on (and end up with the over-all transfer function). I kind of think that that is also the intention of this exercise.
As far as I can see you skip over a lot of things that are pretty essential. There is no way I can approve of e.g. T_{eq}(s) = 4T(s) because there is so much in between. But I would have no trouble at all with ##4\Theta_{eq} = \theta_{in}##. That's what gears do for a living.
Let's define ##\theta_1## input axle, ##\theta_2## intermediate axle, ##\theta## central pinion axle, and
##T_1## torque on ##N_1=10##, ##T_2## torque on ##N_2=20##, ##T_3## torque on ##N_3=30##, ##T_{eq}## on central pinion.
Furthermore ## D_2 = 1 ## Nms/rad on the intermediate axle, ##D_3 = 1 ## Nms/rad on the central pinion axle,
## I1 = 3 ## kg m
2 of the input axle, ##I_3 = 3 ## kg m
2 of the central pinion with ##R_3 = 2 ## m.
There are easy intermediate conversions ## \theta_1 = 2\theta_2 =4 \theta ## and ##T_2 = 2 \ T1, \ T_{eq} = 2 \ T_3 ##.
Focusing on and working towards the central pinion we can write a bunch of steps in series (I am brainwashed in the time domain, so I start with that):
$$ T(t) - I_1 \ddot \theta_1 = T_1(t) \quad T_2(t) - D_1 \dot\theta_2 = T_3(t) \quad T_{eq}(t) - I_3 \ddot \theta - D_3 \dot\theta = -R_3\ F(t)$$ This should ultimately give the transfer function for ##T(s) \rightarrow T_{eq}(s)\rightarrow F(s)##.
From there to the mass M:
$$F(t) - M\ \ddot x(t) - D_M\ \dot x(t) - k_M\ x(t) = 0$$ Then transform to the s-domain and start writing things out. ## F(s) \rightarrow x(s)## is the easiest part. (Sorry, no time left

).
Some comments: "reflecting zzz onto qqq" seems a dangerous business to me. I wouldn't do it: some things can 't be added up directly; they might be terms in a polynomial that must be multiplied with other polynomials later on. But maybe it is unavoidable here.
To answer some of your questions:
J_{eq}s^{2} and D_{eq}s point in the opposite direction as T_{eq} and θ because they counteract T_{eq}: For the torque left over to move the rack (in the negative x direction !) One has available T - D - J = R F (see above).
Note I have a minus on the righthand side as well: Force on the mass M is
up (negative x direction) if torque is positive.
D and J point in the opposite direction as θ because we defined positive ##\theta## and positive T_{eq} as clockwise. (And T_{eq} is the torque
on the central pinion in my interpretation).
The sign of the force on M is determined by the choice for the positive x direction: down is positive. Spring does ##F = -kx## and damper does ##F = - D \dot x##. Inertia is negative if F
on the block is positive: ##F_{external} = M\ddot x ## hence ## F_{inertia} = - M\ddot x## all three together: ##F_{external} + F_{inertia} + F_{damping} + F_{spring} = 0## see above.