Technically, the tense should match, so since we're using the perfect tense (conditional perfect in fact), you should use was.
But both could have ... is and could have ... was are acceptable in this case.
Why? Well, it's because your clause about the paprika being similar to the bell pepper might be true for a long time, and might continue to be true even in the present, so it might be okay to use is.
Maybe not. Maybe the paprika is rotten by now, or already eaten. Then is would make no sense. But a situation continuing to the present would justify use of the present tense is.
Consider:
"I could have gone shopping, because the supermarket was near."
"I could have gone shopping, because the supermarket is near."
If the supermarket has not suddenly moved, it probably still is near – it is now, and it was then – so either one is acceptable.
But some things do not last so long:
Correct: "I could have stayed longer, because it was early in the morning."
Incorrect: "I could have stayed longer, because it is early in the morning."
Unless you are describing something in the very recent past (minutes or hours ago), the fact that it is now early probably has nothing to do with the situation in the first half of that sentence, so mixing the past and present tense in this last example doesn't really work.
Should is never certain; it indicates a correct or expected action to be taken.
Must indicates a requirement.
The only problem with your sentence is that by adding be to the modal verb, must be and should be weaken the certainty, and indicate that the speaker is guessing or making a deduction. I'm not sure when this connotation came into being; the literal meaning of must be and should be is strong, but sometime we started to use must be and should be as a weaker expression of certainty.
(This is covered in the Wikipedia article on modal verbs; epistemic modality indicates a degree of belief, whereas deontic modality indicates a degree of requirement.)
The strongest modal verb in English is shall; it's rather formal though.
If you just want to express certainty but not cause, it's fine to say He will be coming tomorrow.
Best Answer
Wikipedia has reasonably good coverage of modal verbs.
Must is stronger than will: must indicates a requirement, whereas will indicates a prediction of future action without regard to its cause. If someone will do something, we don't know whether it's because they have to, or they want to, or it's just a matter of circumstance.
See also RFC 2119 which outlines the specific meanings of the modal verbs MUST, MAY, SHOULD, and SHALL in requirements documents that cite RFC 2119.