Is the riser on the passenger side? I'd cut the old Y pipe just past the Y, then see if it has the same issue. If it does, then i would question the manifolds. Of course, I think it would be hard to believe the manifolds were that off. Even Chinese manifolds have to be closer than what you describe. I would think Dorman would fit very close to stk. Years ago, I installed cheap no name chinese manifolds and the walker Y pipe fit properly. You want them to fit right so you won't have any problems if the exhaust or engine has to be removed in the future. Forcing the Y pipe on could also create a leak.
After reading about the problems you had with the motor mounts, I'm curious, how did you determine where the rear motor mounts were supposed to go?
The Dorman manifolds aren't great - they also conflicted with the block, initially. I had to grind down the casting to get them to clear and sit flush. I also had to clearance the castings around almost every bolt hole to get the manifold bolts to actually fit. All-in-all, not super impressed, and I wouldn't be surprised if the castings were off.
With regard to the motor mounts - this is a serious mystery to me. The frame was leveled prior to installation (jacked up and checked for level both across the front and rear cross members, and fore and aft on the side rails. I located the front mounts at about where the Downey manual recommends (19.5" from front cross member) then, loaded the old 283 block, bellhousing, transmission, and transfercase back into the truck on a load leveler. Once I got it where I wanted, and at the proper angle (about 4 degrees tilted rearward) I tacked in the front and rear mounts, then set the engine down on them, and made sure everything sat level side-to-side, and at the appropriate tilt. At that point, everything looked good. Looking at the mounts on the frame, everything looks pretty "dead nuts" even when looking at the positioning of the mounts on the frame. It's not like one mount since massively lower or higher than the other.
When I installed the new engine this time around, the truck was on its wheels, and everything was fully assembled (starter, gears in the T-case, clutch components, etc.) so it was probably a heavier load by a hundred or so pounds. I wonder if it may have something to do with weight distribution on the driveline. With the starter and transfercase hanging to the passenger side, there is a LOT more weight hanging out there. The rear mount on the passenger side was hard to squeeze an engine cushion under, while the AA propeller mount at the driver's side was angled up so high it was hitting the support brace on the tub. What's weird to me is the FRONT passenger side mount had the same issue as the rear driver's side mount - sitting high over the cushion by about an inch.
To me it seems like either the driveline is somehow twisted (which seems virtually impossible) or the frame is tweaked (which seems a lot more probable).