I've fitted a new fuel injection system (MegaSquirt) to the old car - the
original was analogue and rather crude.

It's working well but has an interesting side effect. There is an OBC
which calculates fuel consumption etc which is now wildly out. It works
by counting the time one injector is open to give the fuel usage. The
MegaSquirt uses PWM with flyback current limiting to drive the injectors
which I'd guess confuses it.

Any ideas on the best way to convert those pulses into a suitable signal?

What kind of a signal do you need, or think you need? What would be
suitable?