Full disclosure: I haven't read through the lecture notes that your provided particularly carefully, but I think I can answer your question.
Edit: Heads up, by not carefully reading the link provided by the question, I missed something.
The standard New Keynesian models (such as the one Gali presented) are modeled without growth. If you write down the model then you can represent it as a difference equation:
$$0 = E_t \left[ F(X_{t+1}, X_t, X_{t-1}, Z_{t}) \right]$$
where $X_t$ contains all relevant variables and $Z_t$ represent the shocks to the economy. The "steady state" typically refers to the state of the world where $X_t$ is constant (think stable solution to a difference/differential equation) and $Z_t = 0$, thus you could write it as the solution to:
$$0 = F(X, X, X, 0)$$
in which case $X$ would be the steady state value (notice not time subscripts --sometimes also done by denoting steady state with overhead bars $\bar{X}$). This is what he is calling $Y$ and it is a constant value.
For the second question, I haven't read carefully, so I can't be 100% sure, but typically when a variable is written as $X_t$ it references the actual value that is taken (aka if you solved the model and simulated it exactly, this is the value it would have).
For the third question, I think a deeper understanding of log-linearization will answer it for you. Log-linearization at its heart is just a Taylor expansion around the steady state. Consider a generic equation $f(X_t, Y_t) = g(Z_t)$. There are 3 basic steps to log-linearization (refreshed my memory here).
- Take logs
- First Order Taylor Expansion
- Algebra
We first take logs,
$$\ln(f(X_t, Y_t)) = \ln(g(Z_t))$$
If we do a First order Taylor expansion around the steady state, then we can write:
$$ \ln(f(X_t, Y_t)) \approx \ln(f(X, Y)) + \frac{f_x(X, Y)}{f(X, Y)} (X_t - X) + \frac{f_y(X, Y)}{f(X, Y)} (Y_t - Y)$$
$$ \ln(g(Z_t)) \approx \ln(g(Z)) + \frac{g_z(Z)}{g(Z)} (Z_t - Z)$$
Thus we can write:
$$\ln(f(X, Y)) + \frac{f_x(X, Y)}{f(X, Y)} (X_t - X) + \frac{f_y(X, Y)}{f(X, Y)} (Y_t - Y) \approx \ln(g(Z)) + \frac{g_z(Z)}{g(Z)} (Z_t - Z)$$
Recall that in the steady state $f(X, Y) = g(Z)$ and I will also multiply by one in several places ($\frac{X}{X}$ etc...), so
$$\frac{X f_x(X, Y)}{f(X, Y)} \frac{(X_t - X)}{X} + \frac{Y f_y(X, Y)}{f(X, Y)} \frac{(Y_t - Y)}{Y} \approx \frac{Z g_z(Z)}{g(Z)} \frac{(Z_t - Z)}{Z}$$
Now define $\hat{x_t} := \frac{(X_t - X)}{X}$, $\hat{y_t} = \frac{(Y_t - Y)}{Y}$, and $\hat{z_t} := \frac{(Z_t - Z)}{Z}$. This is the percentage deviation of $X_t$ from $X$ (and correspondingly for $Y_t$ and $Z_t$). Then you can write the log-linearized equation as:
$$\frac{X f_x(X, Y)}{f(X, Y)} \hat{x_t} + \frac{Y f_y(X, Y)}{f(X, Y)} \hat{y_t} \approx \frac{Z g_z(Z)}{g(Z)} \hat{z_t}$$
Two final things. First, one subtlety that caught me off-guard the first time I was switching between percent deviation and true values and you might want to be aware of; values that aren't normally negative can be negative because it just means that it is that percentage below steady state. Secondly, functional forms usually make these simplify quite nicely as you have probably seen in the log-linearized equations presented.
In this example, Gali is using $y_t := \log Y_t$ as seen in the other answer, so hopefully this provides some intuition for what is happening elsewhere.
Hope this helped.