I've toyed around a little bit, but I can't seem to get a consistent fix. I tried using an unused field for the Series Abbreviation (I think it was URL), but that sometimes didn't stick.

I wasn't able to set the collection title as the "extra" field in the footnotes, but use the collection title as "series" in the bibliography. It was one or the other.

Ok, so edited:

<macro name="collection-title">
<text variable="collection-title"/>
<text variable="collection-number" prefix=" "/>
</macro>

to be

<macro name="collection-title">
<text variable="extra"/>
<text variable="collection-number" prefix=" "/>
</macro>

but it doesn't read the "extra" field, it's just blank. I used the "URL" field because it would copy in.

Regardless, whatever I had listed as the collection-title in this macro was set for the bibliography.

Here are the footnote markings:
Original (Collection-title)
John M. Allegro, ed., Qumran Cave 4: I (4Q158-4Q186) (Discoveries in the Judean Desert 5; Oxford: Oxford University Press, 1968).

Desired
John M. Allegro, ed., Qumran Cave 4: I (4Q158-4Q186) (DJD 5; Oxford: Oxford University Press, 1968).

Ok, so that works for the footnotes, but not for the bibliography:

n:
John M. Allegro, ed., Qumran Cave 4: I (4Q158-4Q186) (DJD 5; Oxford: Oxford University Press, 1968).

Bib:
Allegro, John M., ed. Qumran Cave 4: I (4Q158-4Q186). DJD 5. Oxford: Oxford University Press, 1968.

It looks to me like the Bibliography just takes the macro from "collection-title" and uses that for the bibliography. How do I separate the two?

ok, I think I got it:

<macro name="collection-title-note">
<text variable="note"/>
<text variable="collection-number" prefix=" "/>
</macro>
<macro name="collection-title">
<text variable="collection-title"/>
<text variable="collection-number" prefix=" "/>
</macro>
***brk***(This was the only other place that used collection-title)
<macro name="issue-note">
<choose>
<if type="article-journal">
<text variable="volume" prefix=" "/>
<text variable="issue" prefix=", no. "/>
<text macro="issued" prefix=" (" suffix=")"/>
</if>
<else-if variable="publisher-place publisher" match="any">
<group prefix=" (" suffix=")">
<group delimiter="; " suffix="; ">
<text macro="container-contributors-note"/>
<text macro="locators-note"/>
<text macro="collection-title-note"/>
</group>
<group delimiter=", ">
<group delimiter=" ">
<choose>
<if variable="title" match="none"> </if>
<else-if type="thesis speech" match="any">
<text variable="genre"/>
</else-if>
</choose>
<text macro="event"/>
</group>
<text macro="publisher"/>
<text macro="issued"/>
</group>
</group>
</else-if>
<else>
<text macro="issued" prefix=", "/>
</else>
</choose>
</macro>

And for the bibliography

<bibliography>
<option name="hanging-indent" value="true"/>
<option name="et-al-min" value="6"/>
<option name="et-al-use-first" value="6"/>
<option name="subsequent-author-substitute" value="----------"/>
<option name="entry-spacing" value="1"/>
<sort>
<key macro="sort-key"/>
</sort>
<layout suffix=".">
<group delimiter=". ">
<text macro="contributors"/>
<text macro="title"/>
<text macro="description"/>
<text macro="secondary-contributors"/>
<text macro="container-title"/>
<text macro="container-contributors"/>
</group>
<text macro="locators"/>
<text macro="collection-title" text-case="capitalize-first" prefix=". "/>
<text macro="issue"/>
<text macro="locators-newspaper" prefix=", "/>
<text macro="locators-journal"/>
<text macro="access" prefix=". "/>
"/>
</layout>
</bibliography>

I know there is a desire to be elegant with the code, but this seems to work:
Fn:
John M. Allegro, ed., Qumran Cave 4: I (4Q158-4Q186) (DJD 5; Oxford: Oxford University Press, 1968).
Bib:
Allegro, John M., ed. Qumran Cave 4: I (4Q158-4Q186). Discoveries in the Judean Desert 5. Oxford: Oxford University Press, 1968.

Thanks! Is there a way I can go about suggesting this to other people? There has been some chatter looking for Series Abbreviations in the forums already.

I have another question regarding abbreviations. Most biblical studies encyclopedias are given abbreviations in footnotes, but are not in bibliographies. So the proper footnote for

Ulrich, Eugene. “Daniel, Book of.” Pages 171-174 in Encyclopedia of the Dead Sea Scrolls. Edited by Lawrence H. Schiffman and James VanderKam. New York: Oxford University Press, 2000.

would be
Eugene Ulrich, “Daniel, Book of,” //EDSS// 171-174.

Is there a way to do that naturally in Zotero? That seems like it's going to be a lot of editing.

My understanding is that if/when CSL gets support for journal abbreviation lists, then this should be doable as well. Frank could probably confirm this, but in that case biblical journal styles could specify lists of biblical studies encyclopedias and accepted abbreviations. If so, this might happen in the early part of next year.

CSL 1.0.1 introduced a "citation-title-short" variable: http://citationstyles.org/downloads/release-notes-csl101.html#new-variables-container-title-short-and-title-short

It hasn't yet been mapped to a field in Zotero, though.