I have both the downloaded PDF manual and the Clymer paper manual. I seriously prefer the Clymer, as it explains things a lot better. And it has a lot of helpful pointers which can save you a lot of time and trouble, and help prevent damage to both you and the bike. It was written for the do it yourselfer, while the oem manual was written for Kawasaki mechanics.
As for as the engine goes, I HIGHLY recommend Roach's videos. He did an outstanding job, and makes everything crystal clear.
Roach's You-Tube Video's by title.
1985 Kawasaki Vulcan Engine Rebuild
Pt.1 - Removing & Disassembling Heads
Pt.2 - Removing Clutch, Starter Gear, Right Balancer, Right Cam Chains & Sprockets, Rear Cylinder, Stator & Cover
Pt.3 - Removing & Cleaning Valves, Removing HLA oil filter, Cleaning Heads
Pt.4 - Removing Flywheel, Left Balancer, Left Cam Chains & Sprockets, Front Cylinder
Pt.5 - Removing Final Drive, Damper Cam, External Shift Mechanism Cover, Oil Filter Plate
Pt.6 - Removing Pistons, Engine Case Bolts, Splitting Engine Case, Removing Crank Shaft, Transmission, Oil lines,
Pt.7 - Removing Water Pump Shaft, Water Pump Mechanical Seal, Oil Pump Sprocket & Chain, Balancer Shaft, Oil Pump, Left Side Oil Pipe, Oil Pressure Relief Valve, Oil Passage Cover, Shift Drum, Shift Mechanism, Tie Rod & Shaft
Pt.8 - Bleeding HLAs, Checking Tolerances on Cam Shafts & Cam Shaft Covers
Pt.9 - Checking Tolerance on Heads, Cam Shafts, Cam Chains, HLA Leak Down, Valves, Valve Guides, Valve Seats
Pt.10 - Checking Tolerances on Valve Springs, Cylinders, Pistons, Piston Rings
Pt.11 - Checking Tolerances on Clutch Plates, De-glazing Clutch Plates, Checking Tolerances on Oil Pump
Pt.12 - Checking Tolerances on Crankshaft, Transmission, Honing Cylinders
Pt.13 - Lapping Valves
Pt.14 - Drilling Clutch Hub (Fix Coffee Grinder Noise), Installing Valves
Pt.15 - Installing HLAs, Rocker Arms & Springs
Pt.16 - Installing Oil Pump, Balancer Shaft, Oil Pump Chain & Sprocket, Oil Passage Cover, Oil Relief Valve, Oil Lines
Pt.17 - Installing Internal Shift Mechanism (Tie Rod, Shift Shaft, Shift Arm), Oil Pump Chain Guide, Oil Return Line, Water Pump Mechanical Seal, Water Pump Impeller & Shaft.
Pt.18 - Installing Shift Drum, Gear Position Lever, External Shift Mechanism Cover, Transmission
Pt.19 - Install Crankshaft, Combining Crank Case Halves, Oil Filter Plate, Starter Idler Gear, Right Side Balancer
Pt.20 - Install Left Side Balancer, Flywheel, Pistons,
Pt.21 - Install Cylinders, Cam Chains, Cam Chain Guides
Pt.22 - Install Heads and Spark Plug Retainers
Pt.23 - Installing Cam Shafts, Setting Cam Chain Timing, Installing Cam Cap, Cam Chain Tensioners, and Cam Shaft Cover
Pt.24 - Installing Flywheel, Primary Gear, Pick up coil mod, Shift Shaft Oil Seal, Left Side Engine Cover, Pick Up Coil Gap, External Oil Lines, Oil Pressure Switch
Pt.25 - Installing Clutch, Right Side Engine Cover, Clutch Cover
Pt.26 - Installing the Exhaust manifolds, Oil Drain Plugs, Carburetors, Starter motor, Final Drive Gearbox. Mounting the engine and starting the bike.