Definitely aim to have the shaft dead straight.
Are you perhaps using wooden engine bearers ? That would be expected with a vintage engine, to cut the vibration from a solid mounted motor. Cut the bearers to be a mm or under size (under-height) and use metal shim / sheet to finally lift the engine into alignment. I guess the engine has four feet, or least four fixing bolts. So stack the shims at each bolt hole, drill through and then bolt up to lock the shims in place.
1000 rpm is pretty slow in vibration terms, but in the very unlikely event that the shaft "whirls" (ie unwanted vibration at a particular rpm) the shaft can be tuned by fixing additional weight to it. EG a piece of 1 1/2" bore tube split and then fixed over the shaft with BIG jubilee clips or, even better, something more strong. This will move the vibration frequency down.