I disconnected the coolant system, clutch, chain, electrics, exhaust and carbs. Then I removed all of the engine mounting bolts both left and right (rear cylinder head, front cylinder head) as well as the lower engine spindle, firstly by removing the nut on the left hand end, and then gently pushed the long spindle through from the left side.
However, it still appears that the engine is secured on the lower engine mount as all of the other holes are slightly out of line. I notice that the lower engine mount has a whats called a mounting bolt and lock nut. Do these have to be removed in order to remove the engine, and if so, do I need a special tool?

Yes, you need to back them off and it does require a special tool.

I usually leave the lower spindle in place and use a scissor jack under the sump and let the engine rotate down once all mounts are removed.

Makes doing it alone a breeze.

you need a castlated socket (nc30 engine removal tool on ebay) or make one with the right size socket and an angle grinder , but the best bet is to buy one from rick oliver which will also do the clutch too, the ones on ebay will do it at about £10, but the tools rick sells are the best bet , its a proper tool and will do the job over and over for a round £25
http://www.ebay.co.uk/itm/HONDA-VFR400- ... 3cbc446869