Three questions... And I'm not trying to discourage you.
One, what is your planned or current exhaust setup?
Two, what do you have for heads?
Three, what do you have for cooling, and what are your plans for a backup system?
The cologne 2.9L is allergic to heat. Deathly allergic. Cooling is your TOP priority even for a daily driver. Ford really screwed the pooch with heat management on a 2.9 for the American vehicles.
In reverse order, then. At a minimum, consider a new if not true dual core radiator (1994 Explorer with towing package and A/C - biggest one that will fit into the stock core support). Or, like I did, a stock (new) radiator and a bypass coolant pump out of a BMW 5 series for when your mechanical one dies and your engine cannot circulate coolant. They're the size of two decks of cards, and for the price of a few T fittings and a boneyard pump, its cheap insurance.
Next is your stock radiator fan. It was great when it was new. Does your viscous clutch still work? If not, EBay fans for a electric 16" puller mounted inside the factory fan shroud, and a 12" pusher out front. Or, a Mercedes C230 dual pusher fits. Your call. Run one as your primary fan, the pusher as an emergency backup for when your primary fails.
Final note on coolant - DO NOT USE A STANT THERMOSTAT. Consider a Motorcraft. Or an UltraStat. One that Ford recommends, or one that fails in the open position when it fails (all thermostate WILL fail. Remember, heat is the Achilles of the 2.9L.
The two biggest heat management issues you're going to contend with are the 86TM heads and the factory exhaust manifolds. I mean every word of the following: IN MY OPINION, FORD SHOULD HAVE BEEN SUED INTO THE GROUND OVER THE FACTORY EXHAUST MANIFOLDS IN THE 2.9L COLOGNE. IN MY OPINION, THE STOCK EXHAUST MANIFOLDS CAUSED EVERY SINGLE HEAD CRACKING ISSUE ON THE 2.9L COLOGNE V6. IN MY OPINION, THE 2.9 COLOGNE STOCK EXHAUST MANIFOLD IS A EXERCISE IN HOW TO RUIN AN ENGINE, AND HOW TO CAUSE ENGINE FAILURE THROUGH NEGLIGENCE IN ENGINEERING AND DESIGN.
Now that my opinion on the factory manifolds are out of the way, the best solution you have is stainless exhaust headers. Spend the money, buy the JBA. Pacesetters do not have a good track record. My brand new JBA stainless manifolds were $250, free shipping on EBay. Someone in the for sale part of the forums has a set of gently used ones for $100. DO NOT WRAP THEM IN HEAT TAPE, THIS VOIDS THEIR LIFETIME WARRANTY.
Remove the lower shroud from your front bumper as well. This allows the headers or manifolds to dissipate heat and keeps your engine bay cooler. Seeing a theme with engineering and design yet?
If you look at your heads, and they have an "89TM" stamped on them, congratulations, you won the 2.9L lottery. Double points if they say "World Products." If they say "86TM" its your call on what to do next. J&C Enterprises in Fairmont, WV builds an incredible set of heads, especially for the money. https://thecylinderheadshop.com/
Heads, manifolds, and coolant are your three primary concerns. After those, you're probably going to want to monitor your oil situation and timing situation. Look into a Cloyes timing kit and a Melling high volume oil pump. You're going to need to supply that compressor with oil, and though the factory one may be adequate, why gamble on a 30+ year old engine?
Pull your valve covers, remove your rockers, and clean the rocker shafts. They're probably packed with sludge and varnish.
IF you can keep the 2.9L cool and well oiled, it is a fantastic little engine. If not, well, see @Bird76Mojo
Following all of this, look on here for a member named @DCinDC
. He built a very successful turbo 2.9L. My current build is for a supercharged 2.9L. I am still in the phases of getting the engine prepped for the blower, and I am on the computer portion as of recent weeks. My truck is daily driven, so my build is taking the scenic route. @deathbypsi
is one of the resident computer/ECU gurus. Look for his posts and youtube videos. The man is a wealth of information.
I have electronic copies of the bibles for building the 2.9L: Sven Pruitt's V6 builders book, the Ford ECU book, and a few others. I will post links to them if you need them. Read them cover to cover. The Cologne family of engines are European designed and built. This ain't your daddy's 302. They're unique and a challenge to build, but very rewarding when you do.