I have actually had the exact same experience. In my case, I had crew on hand to help me deliver the boat to it's new home and when we started the engine, there was no cooling water comming out of the exhaust pipe. After some troubleshooting I realized that it was getting blocked somehow within the standpipe. We removed the water lines and ran a bunch of water through it back-washing it to get as much sediment and rust out as we could, and made the trip down Lake MI, watching the exhaust and temp closely the whole time. Once we got down, I had about 2 weeks to figure out a more permanent solution prior to a trip. So I pulled the thing out. In the process of getting it out of the boat, it split open at the elbow at the bottom of the standpipe. It had probably been leaking exhaust and cooling water into the bilge all the way down the lake (which would explain some lethargy on the part of the crew :-) ). By this time it was pretty obvious that a major overhaul of the exhaust was going to be needed.
Unlike your situation, I was able to separate the flange from the manifold. I assume your difficulty was in getting the bolts out, as they have a tendancy to rust in there pretty bad. I heated the manifold up with a propane torch and used penetrating lubricant, which got one bolt out. The other one broke, which allowed me to get the exhaust off, but with more problems later :-(.
I did some research at the local Boat US and West Marine (at the time they were seperate), but everybody there was like "Atomic 4? Is that an I/O?", so struck out there. I also struck out on the Ericson owners website, so with time running out I opted to build it myself.
I went to the local hardware store, parts in hand and they were grascious enough to not only cut and thread the pipe for me, but let me put parts together there in the shop so I knew if the lengths would be right once everything was tightened down. I used high temp silicone gasket RTV to seal the threads. It's kind of redish-orange. Seems to have worked pretty well. We used galvanized pipe, which is good except you have to be careful with the fumes when it gets hot as they are pretty toxic. So if your welding on it you have to grind off all the galvanizing around where your going to weld, same for torch cutting. Of course, it's impossible to grind away the galvanizing on the inside, so work in a VERY well ventilated area and keep the open end of the pipe away from your face. Also, when you finally fire it up, make sure you run the engine for awhile with the boat fully ventilated and nobody down below to give it some time to burn off all the oils and anything that might leach from the galvanizing. I'm no chemist or metalurgist, this is just what an old-time farmer told me, and old time farmers are like old time sailors, they're worth their weight in gold.
So I put together the basic structure with the pipe at the hardware store, than I was able to cut the ends off the old standpipe and salvage the outer "shroud" if you will. The standpipe is basically a pipe within a pipe. The exhaust comes from the manifold through the elbow at the bottom and into the inner pipe (I believe it's 2") at the bottom. The best I could tell was that it stays inside that pipe until about an inch or two from the top of the standpipe, at which point the pipe is sort of "halved" to let the gas out and into the top of the larger pipe (believe it's 3"). Meanwhile, the water comes from the manifold through a separate hose and into the shroud part of the way up through that little 1/2" bent nipple hanging off the side. The water gradually fills the shroud and eventually blurbles out through the exhaust pipe, pushed by the pressure of the exhaust gas behind it. You have to be careful not to allow water to backflow down the exhaust into the manifold as this can lead to all kinds of problems including cracks in the manifold or block from shock-cooling.
So I cut a couple "caps" from some scrap 1/4" plate, cut one like a donut so the inner pipe could go through it and be welded to it. I removed about 1/2 of the top end of the inner pipe for about 1.5" or so to create an opening for gas to pass through, but still give me something to weld to the underside of the cap. Than I started welding. It's important for the welds to be good so no water can penetrate the weld, which would lead to premature corrosion. Also, the welds have to hold back the exhaust gas and the water, both of which you don't really want in your bilge. The other challenge I had was getting the flange off the old exhaust system to reuse it on the new one. I ended up having to clamp the old pipe in a vice and heat the flange w/ an oxy/acetelyne torch until it was red hot. At that point I was able to twist it off with a pipe wrench, but only slowly and carefully. Fortunately, the flange has a standard pipe thread, so it will be compatible with the threads that a hardware store can cut.
Once everything was together, I gave it all a coat of high temp black paint (like grill paint) in hopes of protecting it a little better. So far so good, but I'm not in salt water.
The next problem was that pesky bolt that broke off in the manifold. I removed the manifold and clamped it in a vice. I ground the old bolt down flat with the manifold, center punched it as close as I could, and drilled it out. The trick here is to start small and work up. If your lucky, you'll get to a point where you're still only drilling in the bolt, but you've weekend it enough and poured enough oil over it that the remains of the bolt will either thread out or come out in pieces, leaving the original hole, threads in tact. If that doesn't happen, than you'll have to drill out a little bigger and tap it, which means also drilling the hole in the flange a little bigger.
Finally, you'll need some sort of a gasket between the manifold and flange. As I recall, I just used the orange stuff per the instructions as time (and my patience) were running out and I certainly didn't have time to order a gasket, and couldn't find appropriate gasket material in town. It's not a complicated gasket, so I'm sure you could make one if you can find high enough temp stuff, but I'd still coat it with the RTV before you stick it all together. And so far the RTV seems to be working fine.
So mine's all back together and has been working fine for 5 years now. However, this boat still has the problem that if you store anything in the port side locker (where the standpipe is) like fenders, hoses, tool boxes, etc...it will melt against the exposed, uncooled portion of the exhaust system (the part down by the elbow. Ericson tried to get around this by putting a cheesy wood shroud around it and wrapping it with asbestos to insulate it, but it still bit one of my fenders before all this. So I've given up on using that storage for anything other than anchors until I come up with something better.
So for that reason, I too am still looking for a more modern drum style muffler system that will run cooler, take up less space, weigh less, and be quieter (the standpipe doesn't make for much of a muffler). On that note, there may have been baffles of some kind in there initially, but in mine there was certainly no sign of them anymore. If anybody else has any info on that, please add.
So sorry about the long post. It's one of those projects that has a lot of "gumption traps", so be prepared for that. But with any luck, whatever you do will last another 35 years, so you'll be in good shape.
Good luck, let me know if you have any more questions, tell us how it turns out, and certainly, if you find a viable alternative to the standpipe, let me know!!!