Ghost Town Hunter

Just replaced the W56 and transfer case in my '88 4-Runner 22re.
Truck had been sitting for several months. After Everything was complete I couldn't get the thing to turn over. Best I got was a click. Push starts fine but I believe the clutch cylinder still need more bleeding.
So far I have replaced the Battery, Starter and found the wire to the starter from the ignition was bad. At this time the truck labors extremely hard when attempting to start even in neutral with the clutch depressed. Feels almost like the timing is severely retarded but nothing there was touched and when it does catch it seems to run fine even at idle. After 3 starts it has now drained the new battery to the point where it wont turn over anymore.
I'm assuming my next step is to pull the starter back out and make sure that it operates correctly when not engaging the flywheel.
Really stumped.
Any advice?