Which is the guideline to choose a molecular target to identify vertebrate hosts from arthropod bloodmeals?
I have looked about the topic and I have asked experts and the best aproximation to know the vertebrate host from arthropod blood meals is targeting mitochondrial genes because you can get clean sequence data due the fact that only one allele is present rather than two. 

Within the mitochondrial genome, you should select a gene which has been widely sequenced for most vertebrate species you are likely to detect in your region, other wise you will have many unknown identities among your bloodmeals. Really, there are just two choices that match these criteria: cytochrome oxidase I (COI) gene, which has been used by the Database of Life project; and cytochrome b, for which sequences are widely available (i.e. for many vertebrate species) in GenBank. If you get a negative result for one, you can try the other. Primer sequences are widely available in the literature. 

In conclusion, you must be target COI and Cytb genes to assure the host identification and prevent a unidentified match in Database of Life project or GenBank.

I give you a paper example to review the metodology: Host Preference of the Arbovirus Vector Culex erraticus (Diptera: Culicidae) at Sonso Lake, Cauca Valley Department, Colombia