One way to minimize the effects of residual stresses (probably the likely-est culprit threatening your project), whether contained in the "as-delivered" bar stock, or induced by rough machining operations, is to vibratory stress relieve the workpiece. Considering your tight tolerances, it should be done prior to rough machining, and again afterwards.
The rough machining should include not only the removal of the stock that approximates the required profile, but also the drilling of most of the stock associated with the bolt pattern. The stress relief might cause some distortion (usually minimal, over 100", a few 1/1000's" is possible), so, if the bolt pattern needs to be precisely in-line to that degree, leave several thousanths in the holes, which can then be removed with an end mill as part of the final machining.
Some prudence and patience during machining is also advised. Machining setup should include sufficient clamping, and careful monitoring (independent of the machine tool used, such as a laser, suggested by grinderguy) of the part during the clamping. The machinist should be willing to shim that final 1/1000 out, if need be to assure no preload, prior to machining. And watch out for that guy opening a door that brings in a cold draft!!!
By stress relieving the part when it is very close to net shape, and as much as possible of the stock removal accomplished, tolerances are easier to achieve. The longest part done using such methods that I have been involved with, was 714". It was straight within + or - 0.003" over the full length, a ratio a little tighter than your target, but similiar, after final machining and monitoring over a few weeks time during assembly. We have a case study on the 714" workpiece, that I can e-mail to you.
bklauba@airmatic.com