Looks like you are making some great progress Don. I encountered the same issues when installing the TP boxes. Not necessarily more difficult, but did require making a few different special tools vs. the stock boxes. Same with the lifter blocks. I didn't realize I could not get the pushrods installed without removing the lifter boxes. Now that I know, I would alter the assembly sequence next time. (hoping next time will be a different motor on a different bike!!)
Encountering these things and deriving solutions is part of the enjoyment of buliding the motor - or tinkering in general - for me. Adds to the satisfaction when successfully completed... 
The pushrods were a bit of a surprise here Scott. I knew the original ProTaper pushrods would not go in. The ones the chromemoly termites ate. But they were never designed to be quick install. They'd not go in with standard rockers without taking the top off.
When I picked up these HD adjustables I expected they'd sneak in. Happened to do the rear cylinder first and they did go in that one. So I thought, "success." Then the front one would just barely not make it.
If that push rod tube had more clearance to allow more wiggle room it might have. I could get the pushrod by itself in. Just not in combination with the tube. So the lifter block came loose.
Like you I don't mind the little irregularities and pecularities of bringing various parts together. Stuff like butchering allen tools and making assembly options takes awhile; especially the first time. But when it looks right and is right when it's done it is a victory of sorts when completed.