As taken from this site: "http://maaheswari.blogspot.com/2011/01/bilvastakam.html" to match the version sung during Aadhi yogi aalayam consecration ... hope the sequence is right since I don't have the song recorded & with me now.
[Update as of 25 Feb 2012: I have the song now and have updated it per the Trigun album from Isha]
Tridalam Trigunaakaram Trinethram Cha Triyayudham,
Trijanma Papa Samharam Eka Bilwam Shivarpanam
Tridalam Trigunaakaram Trinethram Cha Triyayudham,
Trijanma Papa Samharam Eka Bilwam Shivarpanam
Akhanda Bilwa Pathrena Poojithe Nandikeshware,
Shudhyanthi Sarva Papebhyo, Eka Bilwam Shivarpanam
Saligrama Shilamekaam Vipranam Jathu ChaArpayeth,
Soma Yagna Maha Punyam, Eka Bilwam Shivarpanam
Danthi Koti Sahasrani Vajapeya Sathani Cha,
Koti Kanya Maha Danam, Eka Bilwam Shivarpanam
Lakshmyasthanutha Uthpannam Mahadevasya Cha Priyam,
Bilwa Vruksham Prayacchami, Eka Bilwam Shivarpanam
Lakshmyasthanutha Uthpannam Mahadevasya Cha Priyam,
Bilwa Vruksham Prayacchami, Eka Bilwam Shivarpanam
Darshanam Bilwa Vrukshasya, Sparsanam Papa Nasanam,
Aghora Papa Samharam, Eka Bilwam Shivarpanam
Kasi Kshethra Nivasam Cha Kala Bhairava Darshanam,
Prayaga Madhavam Drushtwa, Eka Bilwam Shivarpanam
Kasi Kshethra Nivasam Cha Kala Bhairava Darshanam,
Prayaga Madhavam Drushtwa, Eka Bilwam Shivarpanam
Moolatho Brahma Roopaya, Madhyatho Vishnu Roopine
Agratha Shiva Roopaya, Eka Bilwam Shivarpanam
Tridalam Trigunaakaram Trinethram Cha Triyayudham,
Trijanma Papa Samharam Eka Bilwam Shivarpanam