William,
I have had some experience transplanting LT1 engines. You mentioned two things I have had experience with.
1. Overheating: Are you running a sealed surge tank that T's off the heater hose line and is higher than the engine for purging the air out? Did you air bleed the air off the engine through the T-stat housing?
2. Missfire/idle: You mentioned the water pump blew. Please tell me NO water of any kind got on your opti-spark. You might want to go ahead and pull the opti and at least remove the cap portion and make sure it is clean, dry, and corrosion free inside. If it is not a new unit, at least a cap and rotor kit would be a good idea.
I enjoyed watching the video. You are going to have a blast.
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