Following is a response from Senior DHS staff member, Tom Pullum:
The following Stata lines work for this merge (at least for me). I only include a few variables--you will want to revise to include more. You could put a line before "save MRtemp* such as "rename mv* v*" so the mv variables for men will be renamed as v variables. I have assumed that you are using the most recent CI survey. Hope this does what you want.
* Specify workspace
cd e:\DHS\DHS_data\scratch
use "...CIIR81FL.DTA", clear
keep v0*
gen in_IR=1
tab1 in*
gen cluster=v001
gen hh=v002
gen line=v003
save IRtemp.dta, replace
use "...CIMR81FL.DTA", clear
keep mv0*
gen in_MR=1
tab1 in*
gen cluster=mv001
gen hh=mv002
gen line=mv003
save MRtemp.dta, replace
use "...CIPR81FL.DTA", clear
keep hv0* hvidx
gen in_PR=1
tab1 in*
gen cluster=hv001
gen hh=hv002
gen line=hvidx
* Merge PR with IR
merge 1:1 cluster hh line using IRtemp.dta
rename _merge merge_PR_IR
* Merge with MR
merge 1:1 cluster hh line using MRtemp.dta
rename _merge merge_PR_MR
save IRMRPR.dta, replace
keep if merge_PR_IR==3 | merge_PR_MR==3
tab in_IR in_MR,m
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