Welcome. Hell of a first post
, sorry to hear you are having these problems. The OEM design of the OPDA on the 05-06 is definitely a weak spot. Most that need a rebuild look at everything from R&R'ing the camshaft on their own to replacement HEMI's with side by side PCM's etc.
Personally, I think a replacement stroker is a solid middle of the road option since it is a straightforward "drop in" and keeps the TJ with its 4.0 heritage. I think 4k for an engine and 3k to install sounds about right to me if a dealer does a typical engine replacement. If mine ever bites the dust (knocks on wood), a stroker is likely what I would do. While it would be nice, I really don't need a 400HP HEMI engine in my TJ! That said, there are pros and cons to all the routes one could take. I like what I see with the Golen 4.6 strokers, but I don't have any first or second hand experience with them. They are also very expensive compared to some of the other 4.0 replacement options. I guess you are paying for the valve cover, other goodies they throw in, along with their experience and warranty. I'd probably be inclined to find a builder that can do something similar for me at a lower cost, or try to do it myself with the engine still in the Jeep if possible.
Have you been able to inspect the OPDA gear and matching camshaft gear wear yourself? Any pics? When I experienced the P0016 on my 05 last year, I immediately replaced the OEM OPDA (LDI Inc.) with the Crown unit. My 05 was a later build and was not in the OPDA recall. It had 103k at the time. My OPDA gear showed a little wear, nothing major, and the shaft had a little play which was causing the wearing issue and the code to pop. My camshaft looked OK from what I could see without removing it. I believe the OPDA gear took the brunt of it (as designed). I've driven around 2k since then on the Crown OPDA without issues, but I do plan to remove and inspect the OPDA every 5000 miles or so to keep tabs on it (every 2 to 3 years for me), unless I hear something funny or pop codes before that.
One other note: About 6 months after the OPDA replacement, I've also added a thin shim (foil washer I made) to pull the camshaft sensor back away from the OPDA tone wheel a tad bit (~0.001-.003"). In very cold weather (0-5 degrees), I was getting a P0344 (Camshaft Position Sensor Circuit Intermittent) on start. After warm, no issues. This is because the tolerances are so tight and the OPDA shaft (with tone wheel) likely wobbles ever so slightly on startup in this drastic condition. Also, the aftermarket camshaft sensors and the newer Mopar sensors to some extent, also have problems operating in the cold without throwing this code. On higher mileage engines, sometimes tolerances become off just a bit and adjustments like this become required (unless you want to rebuild the engine). I've seem manufacturers selling these shims for similar camshaft and/or crankshaft sensors due to the "old age" out of tolerance conditions. This is our only option since we can't adjust the cam sensor "air gap" on the 4.0L.
