Tommy,
Is it possible to find the top dead center of the horizontal pipe in two locations and then use a laser level similar to the one in the link to shoot (you said pipe was too long to shoot a line not sure if you were referring to a laser line level or another means)a line on the horizontal pipe onto the vertical pipe up to the flange and then you can "map" the bolt hole to the center of the 90 when you fab the new spool? If no laser level is available or not feasible for other reasons, soapstone lines on the top of the horizontal pipe and plumb bob from the flange will work too.
I tend to wait on pre fabbing situations like these if any way possible. If you DO get the hole orientation to work...the mating service might not mate up i.e. if you square your flange to pipe, you can't be sure they squared their flange to pipe when they fabbed it, especially since they didn't follow the basic two hole rule.
http://www.lowes.com/SearchCatalogDisplay?storeId=10151&langId=-1&catalogId=10051&N=0&newSearch=true&Ntt=laser+levelSimilar to the Bosch near the bottom left in the link. 199.00
I too hope I understood your dilemma correctly.
Good luck......sometimes it's better to be lucky than good :)