Spectral efficiency improvement is a key focus in most wireless communication systems and achieved by various means such as using large antenna arrays and/or advanced modulation schemes and signal formats. This work proposes to further improve spectral efficiency through combining non-orthogonal spectrally efficient frequency division multiplexing (SEFDM) systems with index modulation (IM), which can efficiently make use of the indices of activated subcarriers as communication information. Recent research has verified that IM may be used with SEFDM to alleviate inter-carrier interference (ICI) and improve error performance. This work proposes new SEFDM signal formats based on novel activation pattern designs, which limit the locations of activated subcarriers and enable a variable number of activated subcarriers in each SEFDM subblock. SEFDM-IM system designs are developed by jointly considering activation patterns, modulation schemes and signal waveform formats, with a set of solutions evaluated under different spectral efficiency scenarios. Detailed modelling of coded systems and simulation studies reveal that the proposed designs not only lead to better bit error rate (BER) but also lower peak-to-average power ratio (PAPR) and reduced computational complexity relative to other reported index-modulated systems.