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I am not sure which flywheel and center hub you are using but there are different set ups. There are some where the hub goes onto the crank flange first and the flywheel on top of it. The others mount the flywheel first and hub second. The starter ring gear winds up in a different place when compared. Pictured are various hub adapters.
Some worked better when installed first rather than the flywheel. Nearly all required a spacer to pull the starter back from the wheel. In most cases the same size as the midplate.



As Fred stated sometimes you have to mix and match because of all the possible combinations of mid plates. I had to make my crank adapter but I'm using jw bell and I think it is a tci wheel.If I read your post right it sounds like the starter snout is getting hung up in the pilot hole. Did you dry fit your starter before you put the transmission in? When I fit my starter on the bench the first time it would not engage all the way. The snout and pilot needed to be cleaned up a bit. I can see having to shim the starter to get the right engagement on the ring gear but the starter should go in tight to the bell housing unless there is interference in the pilot hole.