I've fixed and simplified many thousands of ref and name tags which were either in the old style, had now-unnecessary attributes, or were simply wrong.

There are nearly 200 remaining ref tags which appear to be possibly malformed. This is the list, including some which are obviously OK, retrieved using the XQuery below in the db admin client.

xquery version "1.0";

declare default element namespace "http://www.tei-c.org/ns/1.0";

for $r in 
//ref[not(contains(@target, ':')) and not(contains(@target, '../docs'))]
return (concat($r/ancestor::TEI/@xml:id, ': '), $r)

ONE1: 
<ref target="docs/de%20Certeau,%20Practice%20of%20Everyday%20Life.pdf">.pdf</ref>
ONE1: 
<ref target="../admin">Administrative Functions</ref>
QMPS1: 
<ref target="TOWE5">Tower</ref>
STOW35: 
<ref target="../index_locations.php?type=ward">Wardes</ref>
STOW35: 
<ref target="../index_locations.php?type=ward">wardes</ref>
IYKN2: 
<ref target="ROYA1">Burſe</ref>
IYKN2: 
<ref target="INNE1">Inner Temple</ref>
IYKN2: 
<ref target="LOMB1">Lumber-ſtreet</ref>
CHUR3: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
GALL2: 
<ref target="../guidelines_contributors.php">Guidelines for
                                Contributors</ref>
STMA20: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
LITT2: 
<ref target="../render_page.php?id=LOND2&title=London Stone">London
                            Stone</ref>
LITT2: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
HART4: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
PUDD1: 
<ref target="section.php?id=C6&location=Pudding Lane">C6</ref>
THAM1: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
ELEA1: 
<ref target="ELEA1">Cross</ref>
ELEA1: 
<ref target="ELEA1">Cross</ref>
ELEA1: 
<ref target="ELEA1">Cross</ref>
ELEA1: 
<ref target="ELEA1">Croſs</ref>
ELEA1: 
<ref target="ELEA1">Cross</ref>
ELEA1: 
<ref target="ELEA1">Cross</ref>
ELEA1: 
<ref target="ELEA1">Cross</ref>
ELEA1: 
<ref target="ELEA1">Cross</ref>
ELEA1: 
<ref target="TAYL4" type="bibl"><hi rend="font-style: italic;">A full and compleat
                                    Anſwer</hi> Sig. A4v</ref>
ELEA1: 
<ref target="BREN1" type="bibl">Brenner 450</ref>
ELEA1: 
<ref target="DOWN2"><hi rend="font-style: italic;">The Down-falle of Dagon</hi> Sig. A4r</ref>
ELEA1: 
<ref target="ELEA1">Cross</ref>
ELEA1: 
<ref target="HARL1">Robert Harlow</ref>
ELEA1: 
<ref target="ANDR3" type="bibl">Andrews 144-45</ref>
ELEA1: 
<ref target="WING1">Wing</ref>
ELEA1: 
<ref target="WING1">Wing</ref>
ALDG4: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
HOLB3: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
LOND2: 
<ref target=".../render_page.php?id=ASST1">“A straunge ſighted Traueller”</ref>
WCHE1: 
<ref target="/guidelines_contributors.php">Guidelines
                            for Contributors</ref>
KNIG1: 
<ref type="bibl">Kent 249</ref>
KNIG1: 
<ref type="bibl">Thornbury 281-93</ref>
LOVE1: 
<ref target="section.php?id=C7&location=Love Lane, Thames Street">C7</ref>
GRAC1: 
<ref type="special" target="QMPS1">royal processional route</ref>
CHEA2: 
<ref target="WEIN1" type="bibl">Weinreb 148</ref>
CHEA2: 
<ref target="STOW1" type="bibl">Stow 1:324</ref>
CHEA2: 
<ref target="STOW1" type="bibl">Stow 1:35-36</ref>
CHEA2: 
<ref target="BEBB1" type="bibl">Bebbington 82</ref>
CHEA2: 
<ref target="BEBB1" type="bibl">Bebbington 82</ref>
CHEA2: 
<ref target="STOW1" type="bibl">Stow 1:265</ref>
CHEA2: 
<ref target="BEBB1" type="bibl">Bebbington
                        82</ref>
CHEA2: 
<ref target="WEIN1" type="bibl">Weinreb 148</ref>
CHEA2: 
<ref target="STOW1" type="bibl">Stow
                        1:266-67</ref>
CHEA2: 
<ref target="WEIN1" type="bibl">Weinreb 148</ref>
CHEA2: 
<ref target="STOW1" type="bibl">Stow 1:296, 1:345-46</ref>
CHEA2: 
<ref target="WEIN1" type="bibl">Weinreb 148</ref>
BASI3: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
SUGA1: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
TRIN1: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
CHEA1: 
<ref target="STOW1" type="bibl">John Stow, A Survey of London, 2nd ed.
                            (London, 1603; STC #23343)</ref>
QUAY1: 
<ref target="../section.php?id=D7">D7</ref>
STOW9: 
<ref target="MERR2" type="bibl">Merritt, “Strype’s <hi rend="font-style: italic;">Survey</hi>”</ref>
STOW9: 
<ref target="ARCH3" type="bibl">Archer 21</ref>
THIR1: 
<ref target="STON2" type="bibl">“Social Mobility” 23-24</ref>
THIR1: 
<ref target="STON2" type="bibl">24</ref>
THIR1: 
<ref target="SHAR1" type="bibl">322</ref>
BIBL1: 
<ref target="MANN1">PM</ref>
BIBL1: 
<ref target="#WEIN2">3rd edition</ref>
ALDG3: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
BENB1: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
GREE2: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
LIME2: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
TRAN1: 
<ref target="../index_locations.php?type=church">Pariſhes</ref>
TRAN1: 
<ref target="../index_locations.php?type=church">Pariſhes</ref>
WRES1: 
<ref target="../guidelines_contributors.php">Guidelines for
                            Contributors</ref>
guidelines_contributors: 
<ref target="#suggestedSources">bibliography below</ref>
guidelines_contributors: 
<ref target="#suggestedSources">bibliography below</ref>
guidelines_contributors: 
<ref target="#citationGuide">Citation Guide</ref>
guidelines_contributors: 
<ref target="#citationGuide">MoEML Citation Guide</ref>
guidelines_contributors: 
<ref target="#citationGuide">MoEML Citation Guide</ref>
guidelines_contributors: 
<ref target="#citationGuide">MoEML Citation Guide</ref>
guidelines_contributors: 
<ref target="#citationGuide">MoEML Citation Guide</ref>
class_520_1: 
<ref target="docs/Kagan_Urbs_and_Civitas.pdf">.pdf</ref>
class_520_1: 
<ref target="docs/de_Certeau_Practice_of_Everyday_Life.pdf">.pdf</ref>
class_520_1: 
<ref target="../admin">Administrative Functions</ref>
index_moeml: 
<ref target="street_index.htm">Streets</ref>
index_moeml: 
<ref target="site_index.htm">Sites</ref>
index_moeml: 
<ref target="church_index.htm">Churches</ref>
index_moeml: 
<ref target="topography_index.htm">Topographical Features</ref>
index_moeml: 
<ref target="ward_index.htm">Wards</ref>
index_moeml: 
<ref target="people_index.htm">People</ref>
index_moeml: 
<ref target="litref_index.htm">Dramatic References</ref>
index_moeml: 
<ref target="companies_index.htm">Livery Companies</ref>
index_moeml: 
<ref target="neighbourhood_index.htm">Neighbourhoods</ref>
pedagogical: 
<ref target="render_page.php?id=QMPS1"><title level="m">The Quenes Majesties Progress</title></ref>
pedagogical: 
<ref target="citing.php">cite it appropriately</ref>
links: 
<ref target="../index_companies.php">Livery Companies</ref>
teaching: 
<ref target="docs/Jenstad_London_Grad_Course_2005.pdf">Syllabus (.pdf file)</ref>
teaching: 
<ref target="docs/Clark_London_Theatre_Syllabus_2008.doc">Syllabus (.doc file).</ref>
teaching: 
<ref target="docs/Early_Texts_Assignment.doc">.doc file</ref>
teaching: 
<ref target="jenstad.php">Janelle Jenstad</ref>