Let me start by stating I am not a mechanic but I've done all the work on every vehicle I've owned. I paid a shop one time in my life to rebuild a transmission. $2k and they couldn't even figure out how to reinstall the starter and lost my shims in the process (83 F100 w/302.)
I now have a 2000 Dodge Dakota 3.9 2wd 42RE auto with 180k on the clock. I had installed a new thermostat last summer and just used water because I was too poor to buy antifreeze. Well of course when winter rolled around I completely forgot about the lack of antifreeze and since I had just installed glow plugs in my 7.3 I drove it and left the Dakota on standby. As my luck goes it was a pretty cold winter in East Tennessee and after trying to drive the Dodge I found out I had popped two freeze plugs, one behind the motor mount on the drinker side and one behind the starter. I replaced them with rubber freeze plugs and thought I was good to go. It still overheated so then I found out the water wasn't flowing. I removed the thermostat thinking maybe it was seized. It still wasn't pumping water so I replaced the water pump. After refilling the coolant I checked the oil and found milkshake. Then I noticed bubbles in the coolant when running. Could water get in the oil from changing the water pump? The engine still runs great. I'm assuming it now needs a head gasket from overheating. I did some research and found that while I have the engine apart I should replace the timing chain and guides as preventative maintenance. That got me wondering, if I'm gonna have the intake and heads off, what else should I do while I have it torn down? I saw something about a water pump bypass tube. I have no idea what that is but I'll do it while I'm in there. Also I might port the heads and intake while I have them off.
And then there's the need to change the solenoids in the transmission because it's sluggish going into reverse and third. There's no slippage but I heard you should adjust the bands whole replacing the solenoids. It's a lot of work but so far the parts for all of that are still 1/5th the $1200 cost of a rebuild kit for the 4R100 in my F250 (I will be attempting to do that myself with the help of Transmission Bench on YouTube.) The 3.9 in the Dodge runs great and I ran a tiny landscaping business out of it for 5 years with a 16 foot trailer. The truck is only worth about $1k so I'd never sell it. I'm gonna just keep fixing it to the best of my meager abilities and drive the wheels off it. So what else would y'all suggest I do while I have the engine apart and the trans pan out?

 

id pull every thing apart before ordering any parts as it may have cracked block in the lifter valley area

 

Pull the motor out and see if you have any cracks that you cant see. If it's cracked you will be looking for another block.

 

Unfortunately that won't be an option for me. This is a gravel driveway on a hill kinda job. I'm gonna have to just take the risk on all the work required to diagnose. I should be able to confirm a bad head gasket once I get the heads off. At that point, if it's cracked block, I'll have to just scrap the truck. This is a base model truck worth $900 on KBB so I have to be careful how much I spend fixing it. At this time my options are, fix this Dodge for less money than the truck is worth, or rebuild the 4R100 in my 2000 7.3 F250 for the cost of the rebuild kit (about $1k). If you're gonna be poor you gotta be smart.

 

Freeze plugs aren't really a thing. Those are casting holes. If you froze water in the block it almost certainly is cracked. The thinner portions in the valley are common areas so might pull the intake plenum and you should be able to get a decent look. If I were you I would sell it for a few hundred bucks as a blown engine truck. You'll probably find someone willing to through an engine in it.

 

So what other maintenance should I consider doing while I have the heads, intake, timing cover, and transmission pan off?

 

If your plenum has oil in it you should take the plate off and replace the gasket with a thicker one. Felpro makes some good ones. Leaking plenums are probably the most common issue with the A block style motors of that generation. Not sure if the 3.9 was better but the 318 and 360 were pretty notorious about it. Put a new front main seal on the timing cover. Since you will need to pull it I would inspect the harmonic balancer as well. If the rubber looks like its extruded out you will need a new one. Might need a repair sleeve as well as these ones are mainly held on with friction. Don't use the bolt to start it back in. You can usually tap them in about a half inch with a rubber mallet then from there if you can get atleast 3 or 4 threads of the bolt you can do the rest with that. If its binding up don't force it. Take the bolt out and tap it straight then try again. Don't forget to locktite the bolt before the final assembly. It will walk out without it. You'll probably want to replace the timing chain and gear as well. They stretch over time and cause your timing to be retarded and lose some power. Not a requirement but they are cheap and easy to do with the cover off. Keep in mind that the oil pan gasket and lower timing cover gasket are one piece and will probably be unable to seal well after you pull it. If you can I would drop the oil pan and replace the gasket. On the 4wd models that's a very involved process but the 2wd might be easy. Look at clearance and go from there. As for the transmission I would recommend you adjust the bands as you already planned. Pull the sump filter and back rinse it with a hose. They are just screens so no need to replace. Make sure you put a new o ring and get the old one out. When you replace the pan DO NOT use RTV. Get a new rubber pan gasket. These pans are so thin they will not conform the RTV well at all. Try to keep the old fluid clean and put it back in. Especially if the trans is older. You can run the fluid through a coffee filter before putting it back in to catch any large debris you may have had drop in the fluid.