Following is a response from Senior DHS Stata Specialist, Tom Pullum:
The tricky thing about these merges is that the HW files have the household id as a string. With "describe" you can find that hwhhid is a 12-character string. You then need to extract v001 and v002 from hwhhid. Below I show a trick to help find out which columns are v001 and which are v002. You use destring and substring. I show how to do it with the 2000 survey but the alignment is the same in the 2005 survey.
use "C:\Users\26216\ICF\Analysis - Shared Resources\Data\DHSdata\EGHW41FL.DTA"
rename hwline b16
local li=1
while `li'<=12 {
gen col`li'=substr(hwhhid,`li',1)
local li=`li'+1
}
list hwhhid col* if _n<=20, table clean
drop col*
gen v001=substr(hwhhid,3,7)
gen v002=substr(hwhhid,10,3)
destring v001 v002, replace
sort v001 v002 b16
save e:\DHS\DHS_data\scratch\EGtemp.dta, replace
use "C:\Users\26216\ICF\Analysis - Shared Resources\Data\DHSdata\EGKR42FL.DTA"
drop if b16==0 | b16==.
sort v001 v002 b16
merge v001 v002 b16 using e:\DHS\DHS_data\scratch\EGtemp.dta
tab _merge
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