Most of the HLLV designs that I've seen based on Shuttle hardware, such as this old Shuttle C proposal, keep the same engine geometry as the current Shuttle. The SSMEs are in a fairing but on the side of the ET in a position equivalent to where they'd be if an orbiter were present. They did this to keep from having to perform major and expensive modifications to the launch pads. After the Shuttles are retired, that may no longer be an issue but as long as they're still flying, you need to keep from changing the pads. The Shuttle C was intended to carry the payload strapped to the side of the ET, too. That system could easily fit in the VAB just as current Shuttles do. In contrast, the Ares proposal kept the engine geometry but put the payload on top of the ET.

The Russian Energia booster put their engines at the bottom of the ET and used 4 Zenit boosters instead of 2 SRBs. It was a powerful booster, by some accounts more powerful than the Saturn V. It also had several growth versions planned when the program was cancelled. It shouldn't be too difficult to restart the program. The RD-180 engines are still in production, as are the Zenit boosters. It wouldn't be all that difficult to build the tanks. Perhaps reviving Energia would be more practical and cost effective than developing a Shuttle derivative, especially if it were launched from the Cape. Probably wouldn't happen for political reasons, though.