The kia engine is front sump IIRC, so yeah you'll definately have to swap the pickup tube. (notice I mispelled definately using an "a" instead of an "i" between the n and the t? I'd sell a kidney to shake off that bad habit)
I will say this: Buy the mazda complete engine gasket set for a 99. It's worth it's weight in gold. Nothing sucks more than "new" **** breaking or failing. And it's actually like 190 for everything including the good MLS HG.
Breakdown for a RELIABLE engine:
Get 95-97 kia engine that's in GOOD condition. Preferably one from an automatic (99% sure auto trans engines have a 6500 rev limiter and hence the engine is like "new" as it has never really been worked hard) Preferably, you will pull the engine yourself and can pick and choose the right engine. Mileage isn't everything, though it's certainly a consideration. Reading the sparkplugs will give you a pretty good idea about the health of the engine. So will pulling the valve cover and inspecting for cleanliness.
Perform compression test and LEAKDOWN (read what I just said again) to verify you are buying a good engine not a worn leaky engine. You've already got a worn leaky one. No need to buy another right?
Make note of leakdown numbers.
Remove head, oil pan, pickup tube, water pump, oil seals, and timing belt covers from kia engine.
Install new (note I said new, not old, not rebuilt, not "I bought this last year it doesn't have much time on it") water pump for a miata.
Clearance oil pan.
Install miata pickup tube
With a good torque wrench, retorque all main and rod bearing bolts to tight end of factory spec
Install oil pan using good gasket sealer stuff.
Install new front and main oil seals.
Check deck of block and surface of head for warpage using a straight edge and a feeler gauge. Odds are the block will be perfect and the head will be within spec if has never been overheated. If the head is warped past
spec, it has to be resurfaced flat again. If it's warped, it's because the engine it was removed from was overheated. Have the head chemically checked for cracks at the machine shop that surfaces it.
Use a 99+ multi layer steel head gasket. Mazda gaskets are good and so are Fel Pro. I'm running a Fel Pro and it's identical to the mazda gasket.
Install head and torque to top end of factory spec.
Install new cam seals.
Install new high quality timing belt and miata timing belt covers. I'd suggest replacing the tensioner and idler pullies while I was in there for peace of mind. I say this cause I cheaped out and didn't and now I have an idler making a bad noise. Should seize and break the belt any day now.
New radiator hoses w/ real hose clamps and new belts NOT overtightened are a must too.
You do all of that and you'll have done something. Skimp anywhere, and you're compromising reliability.