Following is a response from DHS staff member, Tom Pullum:
The following lines will do this merge. I did not restrict to household heads with hv044=1, but you could do that. These lines will attach the household head's data to the record for each of the 3,334 couples in the CR file.
Many households do not have a couple in the CR file. There are actually many more household heads than couples. What you were doing was correct; I have only confirmed that.
* Stata lines to merge household head data with with couples, Pakistan 2017-18 survey
* Specify a workspace
cd e:\DHS\DHS_data\scratch
* Prepare a file of household heads
use "...PKPR71FL.DTA", clear
keep hv*
keep if hv101==1
gen cluster=hv001
gen hh=hv002
gen in_PR=1
save PK7A_head.dta, replace
* Prepare CR file
use "...PKCR71FL.DTA", clear
gen cluster=v001
gen hh=v002
gen in_CR=1
merge m:1 cluster hh using PK7A_head.dta
tab _merge
tab in_PR in_CR,m