Never restored an E type before (lots of other English cars though), what an interesting learning curve shall we say 
My '69 S2 2+2 uses spring bonnet hinges. Before I put them on the bonnet fit fairly well, now they are on, wow, it’s horrible. The back sides (“A” post" are pulled in, it does not fully close any more and the gap has grown.
What to do please?
Pat
As I recall (from when I messed with the slotted holes in the spring brackets to get better balance) it is possible for those spring brackets to foul on the engine frame. You might see if this is occurring.
These holes:
Hard to see of course as the fouling will occur with the bonnet almost closed.
There is a good bit of adjustment on the stays where they mount. Did you try loosening all the bolts so the stays can move around and seeing whether the bonnet still fits “fairly well” (I know exactly what you mean)…
John North
1969 S2
It is really helpful to became a three-dimensional chess player Grand Wizard, especially with the bonnet.
27.23 degrees of freedom.
Loosen the spring hinges and see which imparts the greater error: bolt the least-sucky one tight, and get that one to work.
THEN, take on the offending one.
Be prepared for (possibly) hours of what the Brits refer to as, “fettling.”
Buy beer or whisky. Get a contemplation stool.
Report back…
Hi John, yes I loosened off all bolts holding the hinges on so they could slide pretty much anywhere they wanted to (up/down) but I’m afraid no joy 
Pat
Is it possible to have them on the wrong sides?
I ended up shimming the lower hinge mounts away from the bonnet to find the sweet spot.
I very much doubt anything to do with spring tension is involved. I have adapted ‘belt and suspenders’ to our bonnet and run a piston as well as the spring hinges. Our bonnet had the mount for the later style and I use an aftermarket piston of the same dimension as a Jaguar unit. As a result, one side has considerably more tension on it (as, of course the later Jaguars with only the piston). This lopsided force has no effect on the bonnet fit. I’d wager you have the air ducts or some other mounting point out of whack so as to really, really bind something up when the unit is lowered. Rather than springs, I’d almost bet the linkage itself is binding, or as Mr. Hahn suggested something is hitting when the springs are installed.
By the way, I did need to modify brackets to use a piston and springs at the same time. My bonnet was too heavy due to lead, my springs were a bit weak and I have no bumpers, motif bar or glass lenses, so I’m light in front and heavy in back.
