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Take the heads. You will need new intake flanges for them to fit right, but only about $20 for a pair. Talk to Scott at Hillside Performance ( a sponsor) about a 98" kit.
Lundee is right about the cylinders but the heads from the 96" motors are much better than the early TC88 heads. Snag them if the price is right, clean them up if they have some mile, SERDI valve job, new guide seals, and install them with a .030" head gasket along with a set of S&S 551 cams. You will need to rejet if carbed or purchase a tuner if EFI. For this upgrade, the Dobeck/Techlusion TFI GEN3 will work but if budget will allow, TTS Mastertune and a dyno tune would be better. You can spank a stock or Stage I 96"er with that setup.
Or, bore the take off cylinders to 95" as Lundee suggests, install with a set of SE cast flat top pistons, follow the same recipe with heads; even better. Change cam choice to S&S 570. You could bore to 98" but then you are limited in piston choices. If you wanted to go to 98", send the take off cylinders to Hillside; they have a pretty good program for boring and fitting Wiseco pistons.
I would take advantage of getting the later heads if they are cheap. They will make a difference on an 88"er if combined with the right cam set. I would not install the heads and run the OEM cams; not worth the effort.
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