side plate questions

Last winter when I still had a little extra money I had my internal machined and bought a unfinished side right side plate, now that I have a little time I've gone through and sorted my rivet set and printed off the build sequence at the top of this page, the plate has some of the holes marked and so far they are not matching up, the cartridge stop is the first one not to line up, but I can't imagine this is very critical, but the marks for the pintle pad don't line up and this I have to believe is very important, will the starter holes mess up my finish holes? How can I drill these holes with out having the drill bit try to follow the marks that don't line up? I hope his machine work on the internals was better then the side plate!