I'm unsure what was wrong, but I ran the command again and now it does seem to work. The command used (in my case) was:
otftotfm -a -e 8r --vendor Typofonderie -fkern -fliga --ligkern="T h =: T_h" --ligkern="a e =: ae" LeMondeLivreClassicPro-Book.otf fmlk8r
The above command removes T and h (if found in sequence) and replaces it with the character T_h, and it also maps a and e --> ae.
The following post is trying to be as complete as possible to cover a few bits beyond the basics to set up a text font to your liking with otftotfm.. possibly longer post
There are a couple of caveats to consider when debugging what's wrong. Assuming you know the basics of otftotfm as covered in How do I use TrueType Fonts with PDFTeX using otftotfm?), the basic command is the same as above, so
otftotfm -a -e 8r --vendor Typofonderie -fkern -fliga --ligkern="T h =: T_h" --ligkern="a e =: ae" LeMondeLivreClassicPro-Book.otf fmlk8r
Important part: the file name specified all the way at the end, fmlk8r (as per the font scheme used for fontinst). I've used fml as the type family name, so my fd file is
\ProvidesFile{t1fml.fd}
[2012/04/22 scalable font definitions for T1/LeMondeLivre.]
\DeclareFontFamily{T1}{fml}{}
\DeclareFontShape{T1}{fml}{m}{n}{<-> fmlk8r}{}
\endinput
I used the following to get the font table and to test some specific ligatures in text:
\documentclass{article}
\usepackage{fonttable}
\usepackage[T1]{fontenc}
%\usepackage{geometry}
\usepackage{microtype}
\pdfmapfile{Typofonderie.map}
\begin{document}
\xfonttable{T1}{fml}{m}{n}
\fontfamily{fml}\selectfont There you go. Some beautiful formulae. Here's a ligature ffi ffl. Therefore.
\end{document}
To check whether a particular character + another character maps correctly to your ligature, check the font table and extract the octal number. In this case it is 240. 24 because of the red box (see below) and 0 because of the blue box (adds up to 24-0). (Remember the octal number of the ligature.)

The next step is to convert your TeX font metrics to property list files. Use the command
tftopl fmlk8r.tfm fmlk8r.pl
to create fmlk8r.pl. Open this with any text editor.
Inside this property list file, you can see if the ligature is correctly mapped by looking up the capital T and checking whether it maps to the ligature. Alphabetic characters simply show up as CHARACTER C <letter>, while all other characters, ligatures and so on, use CHARACTER O <octal number>. In this case we would want to check whether CHARACTER C T has something related to CHARACTER C h, which should map to CHARACTER O 240. In my case it does:
(CHARACTER C T
(CHARWD R 0.615)
(CHARHT R 0.6925)
(COMMENT
(LIG C h O 240)
(KRN O 73 R -0.04)
(KRN O 72 R -0.04)
(KRN O 140 R 0.035)
...
)
)
The line (LIG C h O 240) tells us about a LIGature, which should only be called when the next letter is a C h, and it maps to O 240.
If it doesn't something went wrong at the stage of conversion between OTF and TFM. In that case I would consider consulting the otftotfm manual.
Hopefully this is of use to somebody!
8r. That is intended as an intermediate encoding ('raw'). It is hard to tell as I'm not sure exactly what you are doing but I don't usually use that encoding withotftotfmas opposed tofontinstand, forfontinst, I don't necessarily use it even as an intermediate encoding (although I do sometimes). What you don't want is that the TFMs which are invoked in the font definition files, for example, use the 8r encoding because that isn't a regular encoding for use in a document. (You want T1 or OT1 or LY1 or T2 or TS1 or...) – cfr Jun 07 '15 at 19:47otftotfmbut there are multiple senses or kinds of encodings around. In the creation of fonts for TeX, two of these are of importance. If you are creating virtual fonts, you can use intermediate encodings which are arbitrary and private. There's no problem with doing this. Then there are the encodings of the final fonts which are the ones called in the font definition files. It matters that these are in a standard encoding (T1, OT1, LY1, TS1 etc.). If you are using additional ligs etc., you can vary a standard encoding without doing much harm. – cfr Jun 07 '15 at 19:50otftotfm, just the files are fairly self-explanatory so you only need worry much about the manual. Forfontinst, I always note these changes at the top of modified.etxfiles, for example, as well as in the docs. – cfr Jun 07 '15 at 19:54