Need advice on image processing pipeline

I'm setting up more non-AAVSONet scopes here, which means that I must do my own calibration and processing of images. 

My current methods are not what you could call automated.  (Example:  AIP4WIN, unlike Maxim, won't calibrate an entire folder...looking at FITS header filter names and applying the correct flat frame.  I gotta process all B images, then manually select all V images and process them with a different master flat, etc.) 

Also, if I want to upload processed images to VPHOT, I need to add some FITS keywords with the right values...or VPHOT is not happy.  (Some examples:  TELESCOP = name1, CALSTAT = BDF, USERNAME = name2).

What advice can you give me?  Can Windows software can do this in a streamlined, automated way?  Or should I man up, get a Linux box and IRAF and read the 1500 page manual and build routines/libraries/scripts from scratch?  Or is there another way?

Thank you in advance.