Alexander Berzin has a short writeup on the explanation of lama chopa, especially on combining the three main deities of Tsongkhapa into this practice:http://www.berzinarchives.com/web/en/ar ... ystem.html
I heard that the ganden emanation scriptures (according to Liberation in the Palm of Your Hand) contains preliminary practices such as Jorcho and lam rim instructions (i am not sure, i need to refer back to the text again to verify!), so it does contains in the full path system. There is also the Six Yogas of Naropa being commentated on by Je rinpoche (A Source of Three Inspirations, if i didn't remember wrongly) But if you ask my personal opinion, there is nothing more important than the major indian treatises the Je Rinpoche has recommended, which is (in terms of shastras):
Ornament of Clear Realisation (Abhisamayalankara) by Maitreya, because it contains the paths and grounds of Mahayana;
Entrance to the Middle Way (Madhyamakavatara) by Chandrakirti, because it has a very detailed explanation on Madhyamika, especially (according to Je Rinpoche, the Prasangika's position);
Pramanavartika by Dharmkirti as the foundations for logic and reasoning to study the above text;
Abhidharamakosa by Vasubhandu, the theory of epistemology, and
Commentary on The Vinaya Sutras by Gunaprabha and Shakyaprabha, the moral codes for monastics
Je Rinpoche wrote extensively commenting on these treatisees, and many explanations of the lam rim chen mo has been supported by these texts. This shows the importance of understanding and studying these major indian treatises. On the other hand, for tantra,
Guhyasamaja as the main path as it contains the paths and grounds of Vajrayana, as well as an elaborate treatment on the illusory body;
Chakrasamvra as the detailed explanation for clear light and completion stage practices;
Yamantaka because of its five unique features, and the clearing away of obstacles.
As HHDL has pointed out, there is a reason why Je Rinpoche wrote 5 volumes on Guhyasamaja and less than three pages on Vajrayogini (It's from The Union of Bliss and Emptiness, I need to go find the exact reference) which points the significance or importance Je Rinpoche places on Guhyasamaja. Thus, I would think that the emanation scriptures are more of a skillful means for people who require unique practices (as recommended by one's own Ge-gen), but as for a mainstream Gelugpa, these should be what one should focus on.
Homage to the Mother of Buddhas as well as of the groups of Hearers and Bodhisattvas
which through knowledge of all leads Hearers seeking pacification to thorough peace
And which through knowledge of paths causes those helping transmigrators to achieve the welfare of the world,
And through possession of which the Subduers set forth these varieties endowed with all aspects.
- Ornament of Clear Realisation