A few doubts on PCA and HCA analyses on bivariate Raman Spectroscopy data - data-visualization

Question

I'm an undergrad working on a project, trying to replicate(imitate to be precise) the dendogram and PCA scatterplots as noted from other reference papers.
I have 265 columns of Raman spectra ranging from 401 to 1802 (per-cm). For each observation of the Raman spectra, I have corresponding observations of 30 Test and 30 control groups, belonging to Class 1 and Class 2(Test group indicates the disease, and control indicates healthy data). (Here is a screenshot of how much data I could fit into 1920x1080 haha!)
I did a HCA analysis by just extracting the Test and control data, deleting the top two columns so that I was left with nothing but good 'ol numbers, and deleting the RAMAN spectroscopy column entirely.
Followed standard procedure, used the following code, and got the following output.
import scipy.cluster.hierarchy as sch
from sklearn.cluster import AgglomerativeClustering as HCA
from sklearn.preprocessing import StandardScaler
from sklearn.preprocessing import MinMaxScaler
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
df = pd.read_csv('/home/stormageddon/HCA PCA Analyses/Code/use.csv')
import csv
scaler = StandardScaler()
scaler.fit(df)
StandardScaler(copy=True, with_mean=True, with_std=True)
scaled_data = scaler.transform(df)
import scipy.cluster.hierarchy as shc
import matplotlib.pyplot as plt
plt.figure(figsize=(10, 7))
plt.title("HCA")
clusters = shc.linkage(scaled_data,
method='average',
metric="euclidean")
shc.dendrogram(Z=clusters)
plt.show()
The output looks like this.
So a couple of questions regarding this....
(I followed the exact methods used in Raman spectroscopy literature, i.e Agglomorate clustering, and UPGMA algorithm)
The final finetuned result I was aiming for,is here.(Ref:Barnas.et.al)
So my main points of concern were, in my case the points are overlapping and the graph overall is not looking good. How do I: A]Reduce the number of points to liken it with the ideal image
B]Label the points like those in the image, colourcoded in two colours(for my two classes)?
I did the PCA similarly, but my scatterplot contains points of the same colour.
How do I colourcode the dots in the PCA plot as well?
P.S: I did the HCA correctly right? Or is that part wrong?