It depends on your clicks per second, and the cooldown or desired delay until you re-click.

With the default macro system, you are limited to 255 characters.
And you need to use several characters for the macro itself.
/castsequence reset=combat Name of Spell (That's 39 characters, its safe to assume 30-40 characters for most abilities).
That leaves 255 - 40 = 215 commas in the castsequence.
At 1 click per second, we get 3 minutes and 35 seconds.
At 2 clicks per second, we have 1 minute and 47 seconds.
At 3 clicks per second, we have 1 minute and 11 seconds.

If you use an addon, that will let you use macros of up to 1024 characters.
Which is a lot more commas in the castsequences, for potentially longer delays.

The other thing..
If the long ability is off of the Global Cooldown (GCD), then you can include it anywhere in the macro.
As in, on the main click spam macro, or on any of the called macros, and it will fire off whenever its available.

If the ability is on the GCD, then it will "stick".
As in nothing that is clicked later will execute, when the priority has the "stuck" macro as the next spell and it is still on cooldown.
In that case, you might just want to manually cast it, and not have it as part of your click macro.