I did the exact same thing . i used tons of vise grips and did the complete floor,trunk pan and frames rails . key thing measure the height from every posiion you can think of from the top to the floor pans. i also used the rear cocktail shakers as the refernce to hold the trunk pan in he correct height. leave the inner wheel houses in until the pans are done.
On thing i noticed is the gas tank support rails are welded too far forward on the trunk pan . I removed them and move them back about a 1/4 to contact the tail panel. I clamped everything together, before touching my welder. then i still only tack welded and measured and fit several times before welding it all together. Then after all that is done do one rocker at a time. take my work for it. it took me a long time to do , but my rockers were fine.