Sorry I got super busy these last two days. I've tried converting again, this time using a fan fic so there's no copyright issue with the file. Just to be clear while I am using a fan fic in this instance, it has happened with other pdfs as well. I'm hoping this is what you wanted.
Spoiler:
Convert book 1 of 1 (Buried Secrets, Buried Lies)
Conversion options changed from defaults:
verbose: 2
cover: u'C:\\Users\\USER~1\\AppData\\Local\\Temp\\calibre _f9opmq\\vzfh9j.jpeg'
output_profile: 'kindle_pw'
read_metadata_from_opf: u'C:\\Users\\USER~1\\AppData\\Local\\Temp\\calibre _f9opmq\\gkqbty.opf'
Resolved conversion options
calibre version: 3.25.0
{'asciiize': False,
'author_sort': None,
'authors': None,
'base_font_size': 0.0,
'book_producer': None,
'change_justification': u'original',
'chapter': u"//*[((name()='h1' or name()='h2') and re:test(., '\\s*((chapter|book|section|part)\\s+)|((prolog|pr ologue|epilogue)(\\s+|$))', 'i')) or @class = 'chapter']",
'chapter_mark': u'pagebreak',
'comments': None,
'cover': u'C:\\Users\\USER~1\\AppData\\Local\\Temp\\calibre _f9opmq\\vzfh9j.jpeg',
'debug_pipeline': None,
'dehyphenate': True,
'delete_blank_paragraphs': True,
'disable_font_rescaling': False,
'dont_compress': False,
'duplicate_links_in_toc': False,
'embed_all_fonts': False,
'embed_font_family': None,
'enable_heuristics': False,
'expand_css': False,
'extra_css': None,
'extract_to': None,
'filter_css': u'',
'fix_indents': True,
'font_size_mapping': None,
'format_scene_breaks': True,
'html_unwrap_factor': 0.4,
'input_encoding': None,
'input_profile': <calibre.customize.profiles.InputProfile object at 0x0000000003B8CB38>,
'insert_blank_line': False,
'insert_blank_line_size': 0.5,
'insert_metadata': False,
'isbn': None,
'italicize_common_cases': True,
'keep_ligatures': False,
'language': None,
'level1_toc': None,
'level2_toc': None,
'level3_toc': None,
'line_height': 0.0,
'linearize_tables': False,
'margin_bottom': 5.0,
'margin_left': 5.0,
'margin_right': 5.0,
'margin_top': 5.0,
'markup_chapter_headings': True,
'max_toc_links': 50,
'minimum_line_height': 120.0,
'mobi_file_type': u'old',
'mobi_ignore_margins': False,
'mobi_keep_original_images': False,
'mobi_toc_at_start': False,
'new_pdf_engine': False,
'no_chapters_in_toc': False,
'no_images': False,
'no_inline_navbars': True,
'no_inline_toc': False,
'output_profile': <calibre.customize.profiles.KindlePaperWhiteOutp ut object at 0x0000000003BD6240>,
'page_breaks_before': u"//*[name()='h1' or name()='h2']",
'personal_doc': u'[PDOC]',
'prefer_author_sort': False,
'prefer_metadata_cover': False,
'pretty_print': False,
'pubdate': None,
'publisher': None,
'rating': None,
'read_metadata_from_opf': u'C:\\Users\\USER~1\\AppData\\Local\\Temp\\calibre _f9opmq\\gkqbty.opf',
'remove_fake_margins': True,
'remove_first_image': False,
'remove_paragraph_spacing': False,
'remove_paragraph_spacing_indent_size': 1.5,
'renumber_headings': True,
'replace_scene_breaks': u'',
'search_replace': '[]',
'series': None,
'series_index': None,
'share_not_sync': False,
'smarten_punctuation': False,
'sr1_replace': None,
'sr1_search': None,
'sr2_replace': None,
'sr2_search': None,
'sr3_replace': None,
'sr3_search': None,
'start_reading_at': None,
'subset_embedded_fonts': False,
'tags': None,
'timestamp': None,
'title': None,
'title_sort': None,
'toc_filter': None,
'toc_threshold': 6,
'toc_title': None,
'transform_css_rules': '[]',
'unsmarten_punctuation': False,
'unwrap_factor': 0.45,
'unwrap_lines': True,
'use_auto_toc': False,
'verbose': 2}
InputFormatPlugin: PDF Input running
on C:\Users\USER~1\AppData\Local\Temp\calibre_f9opmq\ msh1se.pdf
Converting file to html...
pdftohtml log:
Page-1
Page-2
Page-3
Page-4
Page-5
Page-6
Page-7
Page-8
Page-9
Page-10
Page-11
Page-12
Page-13
Page-14
Page-15
Page-16
Page-17
Page-18
Page-19
Page-20
Page-21
Page-22
Page-23
Page-24
Page-25
Page-26
Page-27
Page-28
Page-29
Page-30
Page-31
Page-32
Page-33
Page-34
Page-35
Page-36
link to page 41 Page-37
Page-38
Page-39
Page-40
Page-41
Page-42
Retrieving document metadata...
Generating manifest...
Rendering manifest...
Parsing all content...
Parsing index.html ...
Initial parse failed, using more forgiving parsers
Parsing index.html as HTML
Reading TOC from NCX...
Merging user specified metadata...
Detecting structure...
Flattening CSS and remapping font sizes...
Source base font size is 12.00000pt
Removing fake margins...
Cleaning up manifest...
Trimming unused files from manifest...
Creating MOBI Output...
Serializing resources...
Creating MOBI 6 output
Generating in-line TOC...
Applying case-transforming CSS...
Parsing manglecase.css ...
Parsing tocstyle.css ...
Rasterizing SVG images...
Converting XHTML to Mobipocket markup...
Serializing markup content...
Compressing markup content...
Generating MOBI index for a book
MOBI output written to C:\Users\USER~1\AppData\Local\Temp\calibre_f9opmq\ fvfob3.mobi