During my converting a 86 F-250 drivetrain I also converted over most of the brake components from the same truck. I am having trouble getting a decent pedal and am hoping that someone might tell me what I did wrong. I will explain in detail all that I have done and what I am wondering might be possible causes.
I replaced all the lines including the rubber lines with the exception of the rubber line in the rear because it did not look bad to me so that means I replaced both rubber lines that travel from the innner wheelhouse area over to the front wheel cylinders.
I replaced both steel lines in the front also that travel from the master cylinder to the two front rubber lines. What I did on the front is run my line down coming off of master cylinder then I split the two using the original brass block that was on the truck that was attched to the inner frame rail just below the master. I am assuming that it did not matter which hole any one of the lines went into with this block as I am assuming it is nothing more than a split and I am pretty sure that is correct.

For the rear I ran a new steel line from the rear reservoir on the master cylinder down and directly all the way back to the flexible rubber line at the differential end where it again gets split into the wheel cylinders, like I mentioned I did not replace that rubber line, I did replace the steel lines though after the rear junction block going to the wheel cylinders.

I removed and honed out all the wheel cylinders, there are a total of 6 wheel cylinders, I have a single axle in the rear but there are still two cylinders per side, one at the top and one at the bottom of each backing plate. They were pretty rough and new cylinders are 100 plus each so I honed them out the best I could (which was pretty good ). They are nearly flawless but I went thru nearly three of those honing deals you get at Napa that you can attach to drill. I just sat there prob. nearly 1 hour per cylinder in a bucket of kerosine until they were clean on the inside and then rinsed them out with water and then dipped them in the Dot 3 brake fluid that I planned to use in the system. I did not reuse this same fluid in my system I then installed new kits, as far as I have learned the original kits for the rear are unavail, I was given a # by an expert for the correct kit but it was incorrect bore size so I thought to myself that any kit nearly would prob work as long as it had the correct bore size and the boot fit the end of the cylinder so this is what I used. I was able to use a part # given to me for the correct ones in th front and this is what I used there.
The brake pads were already recently replaced, someone had redone the brakes at one time and then the truck just sat again for a long time.

Like I mentioned I used the master cylinder ( which is new ) and power brake booster from the 86, I also coverted the entire pedal/cage assy. The booster is not prefectly flush with firewall at this point because of a rib in the firewall that sticks out and I just did not bother to hammer it down because at the time I figured I would be taking it all apart again anyway sometime soon to do my final work before possible paint. I dont know if the master/brake booster have to sit perfectly level or maybe it does not matter.
In the original 86 system there was a brake proprtioning valve I guess mounted on frame rail below the master cylinder, I did not install this, I did not think I would need it, maybe I am wrong. I have bled the brakes over and over again and still cannot get a great pedal, the truck stops but I dont think it will lock the brakes up, I am thinking the problem is in the rear because when I put a vise grip on the one rear rubber line the pedal is hard as a rock. I dont see any leaks, I am not losing any fluid that I can detect out of the master cylinder, I cannot imagine still having air in the lines but just dont know. Hoping someone has some suggestions.

 

Wow on to the brakes already
My best guess is the rear brake shoes aren't adjusted correctly...... when adjusted you should feel slight dragging when you spin the wheel.
That being said I also see a few other things I am not too sure about in your conversion......
1) you are using a disc/drum master cylinder in a drum/drum setup....... not sure how the larger resevoir will work for drums
2) on that note in its natural habitat, meaning on the truck you took it off the rear, larger resevoir, on the disc/drum master cyinder is supposed to feed the front disc brakes and the smaller front resevoir feeds the rear drum brakes
3) if the booster is sitting crooked on the firewall I have to wonder if you are getting fully travel from the push rod from the brake pedal to the booster... so maybe it is not going out far enough, because of the increased distance from the crooked mounting, to give you full brake pressure.......
4) I also have no idea how things will work without a proportioning valve, some of them incorporate a system to keep a little pressure to the wheel cylinders so the shoes stay close to drums...... which brings me back to the master cylinder you installed may not work correctly on drums vice discs
All of this is just random thoughts on my part and I may well be out in left field, as I sometimes am especially diagnosing something without being able to touch it

 

Thanks, those are great ideas that I will consider and hope to hear some other thoughts, forgot to mention that I have adjusted the brakes all the way out until they drag. I am on everything at once, if I hit a stumbling block I just move onto something else.