This is a partial answer for Q2:
From the Sarvollāsatantram of Shri Sarvānandanātha,
आब्रह्मस्तम्बपर्यन्त॑ कल्पन यन्त्रमात्रकम् ।
तब स्नेहेन वक्तव्यं विशेषस्थ विशेषकम् ॥
अथ विशेषयन्त्राख्याक थनमू--
शालग्रामे मनौ यन्त्रे प्रतिमायां घटे जले।
पुस्तिकायाञ्ञ गड़ायां शिवलिड़े प्रसूनके ॥
We imagin yantra from Bhramha to grass, O devi, for you I say it: shaligram, Beejmantra, yantra, pratima (visual image), Ghat (pot), jal (water), pustika (book), Gada ( like the one with hanuman), Shivalinga and flowers are the things in which we establish/create the yantra (Yantra Nirman). They are special yantras.
तन्त्रान्तरे--
एकार्चनेऽप्येकदेवमेकवारं प्रपूजयेत् ।
एकयन्त्रं कल्पनीयं द्विकल्पे द्वित्वपूजनम् ॥
For puja performed once, let there be only one god. For Worshiping only once, only one yantra is necessary. If there are two yantras worship it twice.
यंन्त्रद्वयम न कर्त्तव्यं तथा मूर्त्तिद्वयं प्रिये।
घटद्वयं न कुर्येयुः साधकाः सिद्धिहेतवे ॥
A sadhaka must never show two yantras for siddhi. Establishing two murti and two Ghat (pot) is invalid according to shastra. (Shastra viruddha)
From Annadakalpatantra:
Apart from the verse given in question. There is one verse taken from linga purana for Shiva puja prayog.
एक पाशुपतं छिछझु मृच्छिलादिविनिरमितम् ।
शालह्ग्रामशिलामेकां गृहस्थइ्चेव पूजयेत् ॥
A Grihastha rather must worship only one Murti or only one shiv linga made out of stone and only one shaligram. (it restricts it only for a Grihastha)
Q2) Also, what are the instructions if the number of Shiva Lingas is more than two say three or four?
Answer: if they exceed, we need to worship them twice.
Matrikabedh Tantra states this, but I dont wether its connected to this question or not. Birthplace is Mahayantra, out of affection never establish another Murti here. If done: Devi needs to be worshiped twice, two times Bali, two times puja, two times japa, twice homa, twice mantra otherwise all goes in vein. Avoid it, never establish yantra here.
Edit: I just realized something, the book Nitya-Karma puja which states that verse from Acharendu is diffrent than in Mantra-Tantra prakash as found in Annadikalpa Tantra. This seems Tantra says something different:
लिंद्गद्वयं तथा नार्च्य गणेशद्वयमेव च।
शक्तिद्वयं तथा सुर्यद्वयमेकत्र नार्चयेत् ॥
द्वे चक्रे द्वारकायान्तु शालग्रामशिलाद्वयम् ।
एतेषामर्चनात्रित्यमुद्वेगं प्राप्नुयात गृही ॥ १७ ॥
This change is in number of Ganesha and Shakti, it's two. Not three. And it does not mention 'Shankha'.
