The intake makes contact pretty quickly, which gets worse with:
1. cam advance
2. more intake lift
3. more intake rocker ratio
4. more overlap
5. smaller LSA
6. head or block mill
The obvious cure is aftermarket pistons with valve reliefs such as shown in the Ross ad picture. Problem: $$$. The stock pistons can be relieved to some degree very carefully since the dome thickness isn't great.
The exhaust has plenty of room.
Yes, the stock pushrods are terrible. The problem is that even 5/16" tubes will rub the clearance holes to some degree especially with more lift (duration doesn't matter).
