Working with a 20 year old boat, you can't assume this is just going to be a plug and play operation.
If it has a wood transom, and it's never been replaced, I'd want to know, beyond ANY reasonable doubt, that it was up for your 90hp conversion. Or better yet, plan in installing new transom wood as part of the conversion.
Then I'd want to know about the engine pod mounting bolts, and where they go through the cross members. Maybe remove a couple of them to see what kind of shape the bolts are in, or any signs of corrosion where they go through. What kind of condition is the pod itself in? Any cracks or deformities? What kind of shape are the cross members in? Bent or deformed maybe?
Clearly the 90 is going to weigh more than the current 50 - and that weight is going to show with the rear of the 'toon sitting noticeably lower in the water. If the water line on the 'toons is already at the half way mark, you may have to put the back of the boat on a diet as part of the project as well. Getting rid of excess weight, or possibly moving it forward are both possibilities.