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The fact that the wood looks good is a good sign. By looking good, I hope you mean that it does not crumble in your fingers
If the drain tubes were rotted, water could get into the transom core. That is not necessarily a serious concern. You should tap all around the transom with a leather or plastic hammer and listen for a nice solid sharp thud. The sound should the same as you move around. to different areas. A dull thud or hollow sound could mean delamination or core rot. You might want to drill a small hole under the trim plate (bang plate) and see what comes out.
What I don't like in the pictures are the cracks and more importantly the brown stains that seem to be oozing out of the cracks. Often, the brown stains indicate rotting wood.
More pictures might help. What exactly am I looking at in the first two photos?
 
I would also be confused when one surveyor said it wasn't bad and the other said the core was rotted.You are probably going to need a fiberglass person to grind out at least one of those cracks to see what is going on. From what you say, it doesn't seem like the transom is rotted but it's hard to really know. You might also want to pull out one of the motor bolts to see how that area looks inside as well as under the inside skin. It's poosible you have an issue towards the top but not all the way down to the keel.
I think pulling a bolt out is the best thing to do at this point
 
A 98 should have rot resistant green board in the transom and possibly an aluminum brace tied to the stringers. I dont think the wood can rot, but it and the fiberglass can delaminate from freezing. Have you stood on the ventilation plate on each engine and looked for flexing at the top or at the bottom of the engine bracket? Place a straight edge on the transom. Has it bowed?
 
My adventure has a rotten transom. I knew it when I bought it and used that as leverage on the price. I am not concerned. I helped a buddy install a motor on a 90's Grady years ago and I was impressed with how thick the glass in the transom was.

What I did was pull the motor and then drilled 1 1/2" holes (4) where the engine mounting bolts go. Filled those holes with glass filled epoxy and then re-drilled the engine mounting holes.

Then I took two 1/4 inch steel plates and epoxy coated them with 3 coats of unthickened epoxy. Plates were several inches larger the the 4 mounting holes on the inside and a few inches larger than the engine bracket on the outside. I painted the plates white as well.

Point of all this is the epoxy filled holes won't allow the mounting bolts to be overtightened and crush the transom and the thick stiff plates distribute the stresses across the transom. I have no cracking and the motor feels rock solid.

Would this work with heavier twins? I don't know for sure but I would try it first before I dropped 5k on an old boat for a new transom.
 
The water doesn't scare me too much. Every 20 something year old transom has some water.
It can be the cause of real problems though
The cracks around the lower motor bolts are an issue because it means its moving or did in the past.
Questions;
How long have you had the boat?
Was work ever done on the transom before? I
In one picture I see some hardened filler that might not be original.
What does the glass at the upper bolts look like?
Does the transom move when you stand on the lower unit?
Have someone watch the lower bolts inside when you stand on it.

I would get into the glass at those lower bolts and look at it good.
I would remove motors (or at least lift them temporarily) to remove the aluminum trim and look in there good.
( a motor jack is $100 at Harbor freight).

It might just be that the glass cracked but the transom is ok.
A little glass and resin and some bigger washers or a plate ....maybe thats all you need

I have replaced a 25 year old transom myself due to some water dripping out screw holes and some soft wood in the corners ...and panic.
It did not flex with the "stand on it" test. There was no cracked glass.
After tearing into it I found the thing would have lasted another 25 years without my help.
It was too late to go back at that point. But hey, I learned a lot and got a project under my belt.

Unfortunately, there is only one person that can make that call. Thats you.
Get as much info as you can.
If you are somewhat handy, its a doable project.
 
When I bought my boat I had a hunch the transom was wet. Pulled the blown motor...and took off the cap. Some areas good. Some areas wet. Probed a bit and found soft spots and glue failure in plywood in a couple spots. Said the heck with it and got out the vibratory tool and chisel. 2 hrs later had it opened up and the wood out. Now, it's possible the boat would have met anyone else's expectations for many years. But, I didn't want to chance it. And, it helped make the decision to enclose the transom and add a bracket. Project was a lot of fun with my Dad. I learned a lot on youtube prior to digging into the "putting everything back together" phase.

I used coosa board and epoxy system 105 from West System. 1708 biaxial fabric with CSM as well. Turned out great.

Hard to give you a picture of what the future brings.

I worked from the inside:
- removed gunnel cap
- cut liner
- Removed inner fiberglass of transom and section of stringers
- Removed wooden coring.
- Used 40 grit sanding disk wheels on 4" angle grinder - cleaned to glass
- Made template and cut 2 pieces of 1" coosa. Bonded them together with mat and epoxy
- Rebuilt exterior cutout area to fill in with fiberglass
- Set coosa in and used 1708 and tabbing and more 1708 and tabbing
- Reset liner and gunnels
- Built new gunnel section mold and made gunnel to fill in.

Some videos of our craziness are located here. Great project. Grinding fiberglass kind of sucked. But otherwise it was fun. I actually keep my eyes open for another project boat.

 
What the heck happened here? Why did this guy delete his post? Was it offensive? You guys put a lot of effort into your responses and now it seems all for not?
 
Likely posted over at THT that he bought a grady with a wet transom. After 10 pages of grady bashing he succumbed to the pressure and an unfortunate fire was the best solution? Just a hunch.

My serious answer is that he is now putting it up for sale and will leave it at that.
 
Ya what the heck, wish these photos and the original post was there. ANTHONYc why did you delete?

I see you only posted once so you're probably not going to read this.