01 versus 99 block differences
 

The 01 added different thrust bearings to the block, and the strengthening effect of bolting the windage tray to the main bearing caps. The compression ratio is 10, versus 9.5, as is well known.
How much difference do the first two items actually make, in relation to planning to build an engine?

That is, I have a 2001 I am going to turbo, but the 125,000 mile engine is old and needs a refresh.
I plan to pull the engine while doing the turbo install.
I have a 1999 block I can build up in advance of pulling the 01 engine, so that I would not be delayed on the reinstall by the process of refreshing the tired old 01 bottom end, when I install the turbo. I will be using 9.5 compression pistons.

How much am I giving up in strength and safety factor by using a refreshed 99 bottom end, versus a 2001? Assume the compression ratio is going to be the same, either way.
Can the ties in the windage tray from the 2001 just be swapped into the 99? Or does it require some special features of the 01 to take advantage of the impact of this block strengthening enhancement Mazda added?

Depends on your goals. For a run of the mill ~250hp build, the blocks may as well be identical. Also, no harm in boosting a 125k mile engine if it runs well currently.

I think you'll need to drill and tap a boss on the block for the VVT oil feed, and the VVT oil pump is much higher flowing.

MSBP requires the 01+ oil pan AFAIK.

Great thanks for that info. Target is < 250 hp.
Engine is blowing blue and consuming oil, and going racing.
I have no qualms about choosing to refresh it.

Are you going to use the VVT head? 01+ blocks feed the VVT from the pressure sensor boss on the block via the hardline, I assume the location/thread of the boss is the same, so you can re-use your 01 hardline. If no, you can use a braided hose to feed the VVT solenoid. I am not sure what the changes are to accommodate the thicker thrust bearings on 01+ (crank, block or both). I would build the 99 block on the side, then swap the pan, MSBP and head from the 01+ on it once the engine is out.

Yes - VVT head, reuse hardline, swap 01 parts onto 99 block, get a new oil pump, most likely the Boundary billet gear high flow pump.
All of that is in the plan.
So I will still have to take some time waiting on refreshing the head.