Engine Mount Issue
I take it that you cannot move the plate down far enough for the front tube to be close enough for the mount to work?
The mounting plate on the bicycle-engines is in fact 2 piece and adjustable. I have the same one and it works well on my Huffy cruiser frame. That is why I got that kit and not the other one. There seems to be two kits out there (for frame mounts, many others for racks) that use the same Honda engine or the lower priced Chinese version. The gearbox is different and the engine mounting plate is different.
If it were me, I would pony up for the adjustable plate. Unfortunately, it costs about $50, so I understand the desire to make what you have work. I would not drill the front tube and just run a long bolt. The engine weighs 12 lbs. and does vibrate even though it is relatively smooth. That will put a lot of shear force on the bolt and it is sure to fail after some vibration. You could try getting some plumbing pipe of suitable size and split it and try using that as a shim, both at the front and back to make it even....but without being there, I really cannot give any good advice.
Sprocket Mount
My kit came with 2 rubber "doughnuts" and two circular plates- one plate was two piece with four holes in one and 5 in the other. The second plate was 3 piece with 3 holes in each. Each individual plate
must make an entire circle. I used both- from the ouside- sprocket, doughnout, spokes, doughnut, plate, plate (to lesen bending of the plates when tightened). I replaced the sprocket bolts with stainless ones of equal size. You must take care to tighten them evenly in a star pattern like you would lugnuts on a car. I numberd the 9 holed with a Sharpie (lacqer thinner takes it right off) to keep track and used a torque wrench, but feel will work fine. I then used a straight-edge laid across the sprocket and confirmed that the sprocket was parallel to the wheel by ensuring that the straight-edge was an equal distance from the rim. Done right, it may affect the dish a bit, but not the true of the wheel.
Fuel Petcock
I would use teflon tape or pipe sealer. However, I chose not to use the petcock. The Honda GXH50 that I have has a built in fuel cutoff and with the frame I have, the petcock interferred and made it impossible for the tank to sit straight. I used pipe thread sealer on all my threaded joints.
Manual Issue
Welcome to the wonderful world of a burgeoning industry dominated by manufacturers with little to no knowledge of the english language or customer service!
I assume you are doing this, but lay everything out first and see where everything goes before you put anything together. It is tempting to dive in, but patience is required. In the end, I used the supplied screws and bolts only to take to Ace to get the proper sized quality fasteners. Doesn't seem like we should have to do this, but the reality is that if you want a good result, that will probably be necessary. Based on the mounting plate you described, the link below is not your kit, but it should provide useful assembly information (look lower on the page)- this is essentially the "manual" that I got.
http://www.grubeeinc.com/USA/4 stroke.htm
They tell you this is a one day, one weekend project. Possible, but not probable if you want something done well.
GOOD LUCK