Feynman's circuit-to-Hamiltonian construction connects quantum computation and ground states of many-body quantum systems. Kitaev applied this construction to demonstrate QMA-completeness of the local Hamiltonian problem, and Aharanov et al. used it to show the equivalence of adiabatic computation and the quantum circuit model. In this work, we analyze the low energy properties of a class of modified circuit Hamiltonians, which include features like complex weights and branching transitions. For history states with linear clocks and complex weights, we develop a method for modifying the circuit propagation Hamiltonian to implement any desired distribution over the time steps of the circuit in a frustration-free ground state, and show that this can be used to obtain a constant output probability for universal adiabatic computation while retaining the $\Omega (T-2)$ scaling of the spectral gap, and without any additional overhead in terms of numbers of qubits. Furthermore, we establish limits on the increase in the ground energy due to input and output penalty terms for modified tridiagonal clocks with non-uniform distributions on the time steps by proving a tight $O(T-2)$ upper bound on the product of the spectral gap and ground state overlap with the endpoints of the computation. Using variational techniques which go beyond the $\Omega (T-3)$ scaling that follows from the usual geometrical lemma, we prove that the standard Feynman-Kitaev Hamiltonian already saturates this bound. We review the formalism of unitary labeled graphs which replace the usual linear clock by graphs that allow branching and loops, and we extend the $O(T-2)$ bound from linear clocks to this more general setting. In order to achieve this, we apply Chebyshev polynomials to generalize an upper bound on the spectral gap in terms of the graph diameter to the context of arbitrary Hermitian matrices.