Looking at your paintshop sketch, the amount you were suggesting to "raise" the shock mounts (lowering the bike drastically) would effectively make the bike handle/steer like a poorly raked out chopper build. Lowering the front an equal amount will restore the rake, but kill your handling due to no ground clearance and severely altered trail measurement. A stock Harley with that rake would steer better because it's triple tree offset and fork length would be engineered to give it the proper amount of trail.
I seriously would weld the shock area back on in stock position with the parts to be scrapped as an alignment jig, then chop off the parts you aren't happy with, then get some nice tubing from eBay or a good metal supplier (or worst case chop up a wrecked or untitled frame for the bare steel stock) and give it the cosmetic look you want.
Sorry to come across as being forcefully opinionated, but I want to see your project end up being something that is a blast to ride, not another ill-handling aesthetics-only build. I REALLY DIG those Zephyr's from a handling/engineering standpoint, but I agree the seat/tail area leaves a bit to be desired.
I was trying to convince my bud to buy a pristine Zephyr 550 @ AMA Vintage Motorcycle Days this past weekend at the incredible 20+ acre swap, but the seat and tail & my wife calling it a "turd" due to that got him swayed to buy an 80 kz550 ltd "cafe" build instead. Cafe meaning rip off seat/gauges/fenders/tank paint, leave kerker 4:1 & Ikon shocks on, throw on clubman bars, aftermarket headlight, & mount a crappy uncomfortable fiberglass surfboard/hump on with a 2x4 & zip ties, & don't re-jet carbs for emgo pods... Was more solid that it's sibling that had a nice brat seat install & terribly short gsxr forks that left the beautiful Yoshi 4:1 1.5" from the ground. Also stock carb jets w/pods&pipe (poorly running)
Are those Mikuni BST31 carbs with the aluminum flatslides? I have a pair from an 89 Katana 600, looked like rad carbs to swap to a vintage bike (673cc gs550/gs650 hybrid in the works)