So are you looking to buy a civic with finished engine so that you can swap your own? What if you find one that doesnt need a swap?
I am sure there are many 1999/2000 civic around with still good running condition engines that will give good performance. Why not just buy that and drive? I am asking because you are concerned with fuel economy as well. If you are looking for power only, then a good b16/b18 swap would do, but when you want a daily drive car, I will suggest you look for a civic in good condition. Will save you time and money.
Other than that, you can go for civic already swapped (if you really dont want the car to have its original engine), and of course have it checked with your mechanic before purchase. For example, there is one being sold with d15b swap, which will certainly give decent fuel economy (depends on its condition of course, which you can confirm with seller).
Just searched out the link for you: https://www.pakwheels.com/forums/cars/251161-f-s-1996-honda-civic-exi-d15b-dual-vtec
Similar to above, I am sure you will find others as well which are properly swapped and wont give you problems due to bad/incomplete swaps.