1. If you bash it too much then you might push the timing cover in slightly which can contact the timing chain/sprockets.
2. The top and bottom sections (like a coke can) won't deform easily thus leaving you with the original problem
3. If you bash the top and bottom sections hard enough they will split away from the casing and more than likely cause a split at the pipe to timing cover which will result in an oil leak.
Best to cut it and re-weld it properly.
Flywheel: The 48 BHP Minor needed 4 bolts. This was deemed insufficient for the higher power 1275 so they used 6 bolts. Using 2 bolts is really not a good idea. If you tune the engine or do and 'sharp' take-offs then you are likely to shear the 2 bolts.
If the engine and gearbox won't come together and there is a 'large gap' then something isn't quite lined up. Pulling the two together with long bolts is not the best solution as you will be exerting a high force on something that is not lined up properly and could well damage something in the process. When you are mating the engine and gearbox, the input shaft splines have to line up with the clutch ones and the end of the input shaft has to enter the bronze bearing that either sits in the end of the crank or in a top-hat housing inside the centre of the flywheel (Ford box to Minor flywheel conversion).
Also, as bmcecosse says, use the correct tools. These bolts have to be done up tight and the chances are that some edges might be slightly less than perfect after all these years so use a tight fitting spanner which will NOT be metric. 5/8", 1/2" and 7/16" AF are the most common spanners needed when performing such an engine/box swap.
Also, a 1/4" Whitworth for undoing prop bolts and gearbox crossmember bolts.
Websites: 
You CAN of course cut a new notch in the 1275 pulley but you'll have to be spot on with it and I don't recommend it for the following reason: It was deemed that the 1275 needed a FRONT engine breather so that's why it has one. If you put a 1098 front cover on then you'll not have a breather and that could well lead to oil leaks. Also, if you have a timing chain tensioner (as a lot of 1275s have) then you'll need to get rid of it or the 1098 cover won't fit!!
When I say "reluctant", I really mean I wouldn't under any circumstances. I'm not altogether fond of my legs/face/life, but they're what I've got, so I may as well keep them 
) It fouled worse than that so my only option was to move the fan forwards and cut the ENDS down so they cleared the radiator header. Odd.