I personally haven't heard of checking the crankshaft endplay at that stage. While installing the crankshaft and lower end of the engine, yes. The only thing that would hold things up is from the input shaft into the crankshaft pilot bearing. The bell housing wouldn't seat if the input shaft isn't in the bearing. Then a matter of it going in so far it bottoms out or hangs up somehow. I personally do measure the input shaft and make sure it's the proper length for the bell housing, which with a common (and the recommended) parts has never been an issue. There's actually a considerable amount of in/out free play in the input shaft/pilot bearing that would prevent the crankshaft endplay from being affected. At least with the combinations I've had experience with. But now that you've confirmed it's OK, all good I guess. What I am surprised about is no one said anything to you about checking the bellhousing alignment. You said the Quicktime and Tremec instructions were basically worthless. But actually as I recall this is mentioned in both. Tremec even makes a point that if this step isn't followed, it could jeopardize your warranty. Almost makes me wonder if the guy from Roush was maybe thinking of this check versus the one you did. Who knows. But this is a pretty big deal. You'll get lots of guys on here that will agree. Plenty of YouTube videos. This one from Summit gives the idea. https://www.youtube.com/watch?v=fxNn4qk_KlM.