NC Miata Possible Rod Knock

About 5 years ago, I bought a 2006 Miata Grand Touring.  It's been a great car for the last 60k miles (~158k on the odometer).  However, it has developed a noise that sounds like a rod knock around 2k-3.5k rpm.  It's less common once warmed up, and it doesn't seem to appear at highway speeds or under heavy throttle.  But, it will knock when I let off to shift.  Sorry, I don't have any audio or video clips of the noise.  I have to get my annual inspection, so I'm going to ask the mechanic his opinion, as well as repair time/estimate.

Is this a common issue on NC's?

I removed the serpentine belt, and the noise is still there in the same rpm range, so I know it's not an accessory.  I need to check the plugs, but when I checked them back in April to see if I could find why my mileage dropped a couple miles per gallon, they looked good.  Though, they are coming up on 60k miles, so it's about time to change them according to the service recommendation, but I doubt that's my problem.

Assuming it's a rod knock, I seem to have the following options:

Rent a car, and try to fix the issue (I assume bad bearings) myself or pay a mechanic, but I'm concerned this will turn into a complete rebuild, which I'm not sure I want to/can spend the time or money on, but mostly the time.  I've found it's getting in shorter supply as I get older.  The money's more of a cost-benefit analysis sort of thing.

Buy a new(er) car/Miata and sell the old one.  What's the going rate for an '06 Miata with an unconfirmed engine racket?

Rent a car with both cars out of service, finally get off my rear and fix the Civic, and then rebuild the Miata (it probably needs the VVT actuator fix as well).

Thoughts?  Especially folks that can give me good news that, "it's probably not a rod knock, and NC's just need 'X' cheap fix."

Buddy of mine had a weird rattle from the front/top end of his '06.  Thought it was the VVT actuator and tore it down to replace.  Turned out not to ba that, or the next thing, finally had it diagnosed as a bad piston.  Yanked out the whole thing and sourced a 2.5 engine to drop in instead.  His car has been down since the spring and is still out of commission.  Apparently the MZR engine is both hard to work on and has some durability problems.  He's not happy.

Sticky lifters?

Thanks for the comments so far.

The VVT noise is only at startup, and I can make it go away by priming the engine (foot on the gas while I turn it over) before startup, so I'm pretty confident that the VVT issue is real too.

Fingers crossed for sticky lifters, but I think the noise is a little too loud for that.

A friend has offered to loan me his extra car for a few weeks, so at least I don't have to drop money on a rental while I figure this mess out.  Tonight I guess I'll start the diagnosis process.  Pull plugs to inspect and check each cylinder with the piston at TDC for play.  Then, it's on to dropping the oil pan and inspecting the connecting rods for play.  Sigh.  This was supposed to be my reliable turn the key and get me to work fun car.  I guess it was for five years.

As far as easy fixes, I think you've discounted most of them. Might just be a lifter/something in the head. Belt tensioners/idler pulleys can sound like that but I'd think it would need a belt.

For the car with a possible bad engine I'd guess $3-4k assuming the rest of the car is in pretty nice shape. I've seen ones with bad paint/interiors and known bad engines go for $2k-ish. Early NCs are creeping down to the $6-7k range with no issues.

There are shops that do 2.5 swaps for relatively cheap, haven't priced them recently but I think $4k-ish all in is about the going rate, Moto-east and Dynotronics are the more well known ones, I think good-win has someone that does them on the west coast as well. They've also put good engines that were pulled by others doing a swap for cheaper as well.

The 2.5 swap itself isn't that difficult, mostly just a matter of getting the right combination of parts to bolt to the long block then dropping it in. I think dynotronics sells parts bundles for DIYers that includes them providing support as you go.  

Rod knock can be found by playing with the throttle.  On and off with no load on the engine.

Could also be piston slap, since the noise improves as the car warms up.  Rod knock would sound harsh when first started but would be more subtle once the cold, thicker oil started flowing.  You'd again hear it more as the opil warms and thins.

I have heard rod knock on an NC, but that was a track-driven car.  In my experience, things that sound like rod knock are unfortunately commonly rod knock.

If that is the problem, used 2.0 MZRs aren't all that expensive so the easy option would be to simply drop a replacement mill in there. The 2.5 swap isn't all that difficult as engine swaps go, but it's still more involved than replacing the engine with an identical one.

I have 2 MZR's in my garage that suffered from Rod knock. Both just about as old as your engine. It's not uncommon. Both made them self known at 2-4K rpm. 

Best bet is 2.5L swap. You can get a light used one for pretty cheap. I bought both for $350 each

The drive home allowed me to hear a slight knock, or whatever it is, even cruising on the highway.  Only driving to and from the shop is in the cards at this point.

From pulling the coil packs, it sounds like cylinder 1 is probably the culprit.  I'll take it the 0.5mi to the local mechanic to get his opinion and quote to swap the engine.  I don't think I have the time or energy to tackle an engine swap right now.

Where would I look to find one of these cheap engines?  Salvage yard?  EBay had a used 2015 for $1800.  That plus the labor kinda kills the cost benefit on a car worth around $6-7k.

Thanks for the comments/info.

Car-part.com is always my starting point for quests like this..

Drop us a line next week. We may have one. The guy who would know details is out for the rest of this week.

Thanks for the replies.  The mechanic agreed it was likely rod knock, but could be a bad wrist pin.  I'll find out soon enough when I dig deeper into it this weekend.

He said the book quoted about 13hrs for engine replacement, which put it in the $1k range.  Not a surprise, but thinking about it, maybe I will get the engine hoist and stand out.  $1k is kinda motivating.

Keith, thanks.  I'll give FM a call Monday to see if you have any MZR motors available for sale.