Se podría creer que se forma el past perfect en frases con un verbo modal de la misma manera en la que se forma el present perfect con un verbo modal pero utilizando el simple past del verbo modal en vez del simple present. Pero no es así. Como ya lo hemos mencionado varias veces, el simple past de un verbo modal sirve para formar el condicional y por lo tanto no se puede utilizarlo para formar el past perfect. Lo que se recibe haciéndolo es un condicional II.

Formación del past perfect con verbos modales utilizando el simple past = condicional II
verbo modal	+ have	+ participio
could	have	gone		podría haberse ido
might	have	done		podría haber hecho
should	have	written		debería haber escrito
needed to	have	read		debería haber leído

Para evitar cualquier ambigüedad hay que construir con una perífrasis.

ejemplos
verbo auxiliar	perífrasis	perífrasis en el past perfect
can =>	to be able to	had been able to
may =>	to be allowed to	had been allowed to
must =>	to have to	had had to
	to be obliged to	had been obliged to
	to be forced to	had been forced to
	to be compelled to	had been compelled to
shall =>	to be to	had been to
will =>	to want to	had wanted to
	to wish	had wished to

Para ver más claro.

Present perfect: I have seen him.
con un verbo modal: I can have seen him

Past perfect: I had seen him.
con un verbo modal: I could have seen him.
=>Es un condicional: Habría podido verlo.

Past perfect: I had seen him.
I had been able to see him.
=> Había podido verlo.