missing baptismal & other records

[Gloria Delgado <gloriad@...>]

All right, here's another problem, actually several questions,  I'm 
putting in the hands of this knowledgeable group:
Over the years we've tried to find my paternal grandfather's baptismal 
record, going through many films of Bautismos in El Sagrario.  I know 
now where and when he was born, as eventually  his civil birth record 
was found under just his mother's name.  His name was Leon CALVILLO 
Ponce, natural son of Jose Guillermo CALVILLO Ursua and Maria Placida 
PONCE Medina.  (His parents, my great-grandparents, were eventually 
married through the Church, in 1875.)
But here's my question:  He should have been baptized sometime in April 
1869.  Although we couldn't find him in any of the relevant books, we 
did come across a mystifying reference to a 'libro secreto #2'  wherein 
(I assume)  were written the entries of natural or illegitimate 
children [Film #299489, Bautismos del Sagrario 1868-1870].   If I were 
to find this libro secreto #2, maybe it would list my grandfather's 
baptism.
Has anyone else come across a reference to this libro secreto #2, or 
does anyone know how to find out more about it?  We asked the personnel 
at the LDS Library, but they didn't have a clue as to what it meant.  
Later on my grandfather went through the Seminary in Guadalajara, and 
studied there intending to enter the priesthood; and I would think that 
one of the primary papers you would need to enter the Seminary is a 
baptismal record.  He would also have needed it for his church marriage 
several years later.  This record  has to be somewhere!  We even sent a 
family member to the diocese of Guadalajara  to ask, but no luck.
 We did find his sister's  baptismal record in La Asuncion [El 
Sagrario] in 1871.  Although she and my grandfather were both hijos 
naturales, she was erroneously listed as una hija legítima of my 
great-grandparents; perhaps that's why she was in the baptismal records 
and he wasn't.
My grandfather and grandmother married in Nuestra Señora de Guadalupe 
Church, in San Francisco, California, in 1904. two years before the 
great earthquake and fire, which as everyone knows destroyed all  
public records.  Luckily the original marriage documents survived, or 
there wouldn't be any legal proof of his marriage either!
 I've been trying to clean up and complete my genealogy as much as 
possible to submit it to this group (and to make Joseph happy).  Should 
I just give up on this baptism as one of those things that will never 
be found?  To make matters worse, I can't find this grandfather's 
grandfather either; and why?  Because two months are missing from the 
records, right where he should have been listed, in July 1816, in 
Aguascalientes, Ags.
Unfortunately the fact is that my genealogy has several 'holes' for 
which I have only oral documentation... (and sometimes not even that, 
just a very strong intuition based on extensive research) and I don't 
have a clue as to what to do about it.  Perhaps just accept it as a 
fact of life and submit what I  have?  No responsible genealogist wants 
to propagate errors, but if I don't turn in what I have, the little I 
do know, and the connections I've made,  will be lost.  What have 
others done in similar cases?  Your thoughts or ideas would be 
appreciated.
Thanks,
Gloria