So, I am now the owner of my first "the anwser". It is a 1999 Green NB, 51K Miles, with an AVO turbocharger setup on it.
I knew there was a mechanical problem with the car before I owned it, but that stuff doesn't scare me very much. The motor has a very clear rod knock sound to it and the plan is the pull the motor and either rebuild the bottom end or swap out a fresh shortblock. I can get a rebuilt shortblock from Treasure Coast Miata for $1200 with no core charge.
Overall goals for the car at this point is to get it running and driving again without making any additional changes as this time. I want to do track days and autocrosses with this car. The performance modifications will come with time. Also, I'm 6'4" which causes a different set of issues I will address later.
I don't know anything about the turbocharger system or what boost was being run. I plan on keeping boost under 10lbs for reliability.
Before I get started anyone have some lessons learned they would like the share?
It's generally pretty easy.. I'd pull the trans & engine out as a unit; I felt that went smoother, but I'm not sure if the time was actually less than dropping the engine in with the trans already in place.. I'm confident there were less swear words, though.
The wiring harness bundle that goes above the starter is a bit of a pain, so make sure you pay attention to how it's routed as you remove it.
Pulling as a unit is definitely easier than just engine. Then upper bellhousing bolts are accessible without a ton of ujoints and extensions. Just use an engine leveler with your hoist.
Thanks for the feedback. One thing I cant find anywhere on the google or the interweb is how long a engine/transmission pull and reinstall usually take. Anyone have a rough guess?
I think I've pulled one in 50 minutes working alone 
That was a few years ago. You'll have to transfer over the turbo system, drill (or swap) the oil pan, change the head... Call it a solid weekend's work if you're mechanically competent. Before you order your short block, check the cam journals for wear. If the oil pressure tanks, they're the first thing to take damage.
About that turbo kit - check the engine management. AVO was using grey-market Link stuff with fairly crap software, and I'll bet your rod knock is a bent rod. You might want to look at replacing the Link piggyback with something else, or at the very least see if you can get a software upgrade for the piggyback. It was a 9 psi kit.
Congrats on the purchase!
I picked up my first Miata Friday, and it also is a green 99. Mine has 55k on it but is entirely stock.
I was glad to open this and see your engine failure wasn't the thrust bearing. My 99 is within the suspect range, and though I have no symptoms that I've noticed, I'm worried it could still happen...
Anyhow, congrats. Any plans for a build thread?
Cooper, if the engine had the bearing problem, you'd know by now. They didn't live past 30k usually. Check the crank end play for maximum peace of mind.
The AVO manifolds also have a bit of a reputation for cracking -- look closely at it before putting it on the new motor. I would definitely second Keith's recommendation to ditch he Link piggyback and go with a more modern engine management solution.
If it doesn't have a coolant re-route already, consider adding one while you've got the motor out. It's WAY easier than trying to get to the coolant port on the back of the head while the motor is in the car, and if you're going to do track days then you're going to want it.
