Looking at buying '84 to'94 truck with high mileage and rebuilding the engine. 300ci 6 cylinder would be the minimum size. What are some reliable engine/tranny combinations ? I'd prefer manual, but I know that is rare.

For that range of years a manual with a six cylindar is not that rare, expecially in two wheel drive. Ford made many F-150 XLT Lariets with 300-6s and five speeds from about '87-'94. If you can't find a stick, the C6 auto is a good choice.