"... I had a few mm sticking out...."
I thought U said it wuz flush.
I would recommend that if I knew....thing is if U don't make those grips very tight
U chew up (destroy) the revealed threads & can't use some other methods of removal.
Congrats!
Glad U decided to mount ur pump w/all its bolts.
Look around the backside (if I remember correctly) of the pump (where it mounts) I think
the block reveals where the long/shrt bolts go.
Use a nail, wire, cut off coat hanger, stick it inda hole'n measure...
Place the "never dry up" style gasket goop on both sides of the gasket. I've had good results w/it.
(Blue tube, red snot inside...1 ada Permitex I believe). Glue gasket on block, test fit pump/bolts,
remove, more snot, replace'n tighten to spec.