Mm... delicious parts.
You'll be fine with the engine. Document the engine number, keep the receipts for everything. You'll need all the emissions components that the Denali had, which your 95 YJ already has. Evap canister with purge control, sealed fuel system, and the computer to control it all (including EGR if the 6.0 has one). You'll also likely need 2 cats.
'91 Frankenheep YJ. 4.0, 4" BDS, Richmond 8.8, Titan 12k, 35" KM2's, rust.
'88 YJ, 4.2/4.0 head, +4½" & shackles, BFG 33's (sold)