We have a '91 250 and a couple of 400 VVC's and the engines/frames are NOT the same. The engine mount points at the cylinder head differ quite a bit. The tank and airbox are different as are the side panels. Look at the angle of the carbs, the 400 carb mounts are just off horizontal, the 250 carbs are REALLY steep. That's why the tank and side panels differ. The frame tube that runs along close to the head is NOT a tube on a VVC engine bike, its only a curved piece of metal that looks like a tube. This allows the VVC system to fit the frame.
Try to get another 250 bandit, Suzuki "Across" or GSXR250 motor (which is what the bandit engine is derived from) as this will be an easy engine swap.
Pete
edit..... I've been trying to find an English manual for a 250 bandit for ages without success. I've also tried looking for a GSXR250 manual also without success. I only recently heard about the Across model and there's a workshop manual available online for that. Same engine as the Bandit and the GSXR 250 (internals are the same but externally there maybe style changes) but different carbs. The Across is GSX250F, google and you should find the manual, it's in English as this bike was sold in Australia and New Zealand.
Click on this link to find LOADS of free to download manuals including the GSX250F (Across) one.
http://www.carlsalter.com/motorcycle-manuals.asp