I did the trunk on my '49 Olds 88 Club Coupe recently. I assume some similarity exists, so I will offer the following. Yes, the piece in the gutter of the body at the top and the piece used on the sides and bottom of the lid differ. I would suggest you get a Steele Rubber Products catalog (800-425-6088) and examine the partially dimensioned profiles in the catalog. Steele will send you free 1" samples of any cross section that looks promising, and you can match them up to your old strip for best fit. Fusick might also send you free samples; they are a good house. I ended up using 11' of Steele 70-0463-85 for the lid and 6' of 70-0412-85 for the body gutter (your 98 will probably use different profiles). Steele sells an expensive molded corner for the ends of the gutter, but you can easily curve the gutter weatherstrip around the corners.
One other thing, I found that I had to install the lid weatherstrip gapped slightly away from the lid flange in order for it not to high center on the body flange and prevent lid closing. I had the same experience with a '49 Cad fastback.