I first recommend that you read the IPUMS-I User Note on “Sampling Error and Variance Estimation” and refer to the bottom of the Sample Design Summary page. The Nigeria samples are drawn by complex stratification with geographic clustering and household clustering. As a result, you should use the household weight (HHWT) as your pweight, use Enumeration Area as your strata, and cluster by household (SERIAL).
As you note, Enumeration Area is not available in all of the Nigerian samples. Not accounting for geographic clustering in these samples will lead to underestimating standard errors, which means you should use caution in interpreting statistical significance at the margins. You might also consider investigating the effect on your standard errors of using State as your strata in the samples without Enumeration Area provided.
Hope this helps.