I am in kinda the same situation. I am putting Fatman's Mustang II IFS and No Limit Engineering Fatbar 4-link in rear.
I am seriously considering starting with the rear first because I am putting an under the bed fuel tank in and I will first make sure it and the rear fit together and then proceed to the front.
Also want to put in a K or X brace and box the frame while I've got it there in the open.
And maybe I just want to avoid fitting motor and trans between radiator and firewall and nothing more...I can't think of much of a difference it makes.
This is a 59 frame, but no incredible differences in the basic ladder frame riveted C-section technology--same as with your 49, for what I know.
Pinion angle you can set in the rear and then weld in engine mounts to match right. So...I don't know that it really makes any difference.
Maybe someone will jump in with some better thoughts, I'm not claiming experience or knowledge here, just some thoughts on how I got to my approach.