An easy way to hold off certain interrupts while allowing others is to use the processor interrupt priority mask in bits 10-8 of the processor Status Register (see 1.5.1 of ColdFire® Family Programmer’s Reference Manual). This field is defined as:
Interrupt priority mask. Defines the current interrupt priority. Interrupt requests are inhibited for all
priority levels less than or equal to the current priority, except the edge-sensitive level-7 request,
which cannot be masked.
You then want to assign (thru the MCF_INTC0_ICR*) your e-port interrupts to use, for example, priority 1, and your clock interrupt (or other interrupts which you don't want to hold off) to use, for example, priority 6.
Then you can hold off priority 1, 2, and 3 interrupts while allowing priority 4, 5, and 6 (and 7) interrupts by setting the processor interrupt priority mask to 3 (in your PauseInt()). You can later restore the mask to 0 to allow all interrupts again (in your ResumeInt()).
One word of caution -- I don't understand the difference between "priority" and "level" in the MCF_INTC0_ICR*, but have never had a problem with just setting them to be the same -- i.e., 6 and 6, or 1 and 1, etc.