I gave up trying to get my roll hoop out - I believe I have the same issue - I have one side of the rim of the grommet disappearing into the hole so was trying to center it and gave up after a couple of hours.
Could you do a pic of where you had the scissor jack ?
Thanks
Graham
Well Graham, I do hesitate to post this photo, but you did ask...

A better method would be to use a ratchet strap from above but while I was fetching the necessary aparatus, my assistant had done the job with his scissor jack. In any case, he was successful!
Both the roll hoop ends and the chassis tubes were crushed to an oval shape and especially distorted around the bolt holes which made them tricky to refit. We used a long half-round file to take off the worst of the burrs around the bolt holes (on the insides of the chassis tubes) and also encouraged the outer hoop receptacle into a 'more round' shape with the aid of a G-cramp. This, combined with a liberal coating with Waxoyl allowed the hoops to slide into position reasonably easily.
The rubber grommets are fairly inexpensive Morgan parts.

11 M370010 Roll Hoop Upper Seal
12 M370009 Roll Hoop Lower Seal
[Note that version 5.2 of the Morgan parts manual is incorrect as it has these descriptions reversed!]