Jeff,
You say you've tried everything. Can you tell me what you've tried? Tim mentions the shims; what about those? There is also the positioning of the softtop in relation to the cars body - as I am sure you've discovered already the holes into which the frame bolts are elongated, not round. There is also a small degree of lateral movement in the frame.
I have recently put a new softtop on my car and had a devil of a time with the softtop gap. However, by removing the shims and playing around with the roof position I got the gap to near zero. The trick, as you have summised, is to reduce to nil that v-shpaed gap on the frame where the window and frame meet. I removed all my shims having put in more than there were. It was a complete bugger of a job, but to me the shim were key. Once I had the gap removed, I then found it near impossible to close the top (big gap at the front where it latches to the windscree). Thereafter I fastened the top at the front and slackened off the soft top securing bolts to allow the frame to find it's own position. This worked. I also had to go back and readjust the window position/height - another crappy job to do twice. With the windows right up, I have to close the door by pushing at the window to make the glass fit into the new rubber seals. However, that does mean that there is no gap. Someone else pointed out that new cars with softtops drop the window on opening and closing the door. I am in effect doing the same thing by pushing the door closed using the glass. Sort of. Also check you have taught wires to keep the wind proof strip in place. They can be quite hard to get tight, but they can take a lot of stress so makesure they're good and hard when the roof is up.
Enough rambling. I have photos of the shims and the whole area if you wish. Let me know.
It is possible to fix. Good luck.
JH