Kodiak 100 pilot reported receiving a low altitude alert on departure when he became distracted by several minor system issues.

Narrative

The aircraft a Kodiak 100 on Amphibious Floats was being ferried to ZZZ1 from ZZZ after being in maintenance for some time. The route was to fly to ZZZZ then to ZZZ1. Weather in ZZZ was marginal VFR with excellent VFR weather in ZZZZ. Getting my weather briefing from Foreflight I filed an IFR flight plan after a thorough preflight. I determined the aircraft was airworthy and computed my weight and balance and takeoff data. The departure off Runway XX called for a climb gradient of 405 feet per nautical mile to 800 feet. Both the Kodiak performance app and Aircraft Flight manual confirmed at my weight the Aircraft would meet that departure criteria. All before and after start checklist were completed and the Garmin 1000 was configured to fly the departure utilizing the GPS in NAV mode and speed being set for the best rate to climb. Takeoff was normal with the aircraft accelerating. I reached down to pull a gear handle up to retract the gear. The gear mechanism is between the seats on the pedestal requiring you to use your right hand to reach down to move the gear lever. I engaged the Autopilot at 400 feet and retracted the flaps which moved slightly but did not retract. I observed the circuit breaker was popped and looked down to reset it however during the maintenance apparently the power lever friction lock was completely in the loose or non-friction position therefore when I took my hand off the power lever; it retarded the engine to flight idle. My initial thought was an engine rollback. The Aircraft begin to lose altitude I disconnected the Autopilot app applied maximum takeoff power. The engine being a Pratt & Whitney PT6 a was slow to respond and I lost several hundred feet during the event prompting a low altitude alert. ZZZ Departure advised a low altitude alert and told me to climb immediately; with high train ahead I deviated to the left and Approach gave me a radar heading. The remainder of the flight was uneventful.