I know it'* a gigantic thread, but I suggest you read through all of this. I did...
For you jake, I don't recommend that you swap the entire 3500. Unless you REALLY want to. If it were me, I would just swap from the heads up. That way you wouldn't have to worry about finding an external crank trigger (currently out of stock) and you wouldn't have to pull the motor out. The only real performance disadvantage will be .1L of displacement and half a point of compression. Not that much IMO. Most of the added HP comes from better flowing heads, UIM/LIM, larger TB (65mm) and better flowing exhaust.
Looking through wot-tech.com, it seems they're out of 65mm TBs and even TB adapters. That really sucks. That makes the 3500 UIM nearly impossible to use. But this could be good news (depends how you look at it), you can still bolt your 3400 UIM to the 3500 LIM and heads. It'* still a performance gain, just not as much as if you went all 3500 top end. Also, if you use the 3500 UIM, you have to buy a fuel rail spacer and FPR spacer, maybe even grind the TB neck a little. So using the 3400 UIM on top of the 3500 LIM and heads would be the cheapest (and possibly only) way to go.
Now the only problem I could see with putting 3500 heads on the 3400 would be pushrods. You MIGHT need custom length pushrods (in stock at wot-tech). Register at 60degreeV6 and ask. I've never seen anything about it, and I know they have the same cams, but it'* best to be sure.