It is quite a common problem on certain miniature loco designs where the cylinder block needs machining at quite a precise angle for the steam chest. If the angle is not correct it throws out the motion plate dimensions and valve gear accuracy.
I have also machined the cyinder blocks of LBSC's Pansy after silver soldering on an additional block on top to avoid the 'bent' blast pipe arrangement and reposition the steam inlet further forward
In my case it was usually the use of a bit of trigonometry plus double check with careful marking out – probably similar to the method JasonB uses.
Cheers,
Julian