The best software for the task would be either Blender or Xismo. While Blender can't export to PMD/PMX as its' own, there is a really cool addon for it called blender_mmdtools (use the powroupi fork, it's really handy). Xismo is a modelling software made for MMDers. It can export (but not import) PMX, but it's missing support for much PMX mumbo-jumbo, thus you're going to need either PMXe or Blender if your computer can't handle PMXe or you don't want to go by the restrictive terms of PMXe. Xismo can draw hair while Blender needs a plugin called AnimeHair to do this task. Best of all, they're both free.
Although Metaseq was (and is still) really popular for its' easy workflow and unintrusive, stupid GUI, you will definitely need to have PMXe or Blender if you don't want to upgrade to a paid version as the basic version excludes important things like rigging and PMX export. Not ideal if you want to exclude PMXe from your workflow, even the paid version as it supports only PMD and you're going to encounter the "Null_xx" glitch as you can't set translations for bones in Metaseq.
Also, make a front and side view reference of your character either on paper or in some kind of software (Blender has a neat blueprinting feature called Grease Pencil) and trace over it in your 3D software of choice. You can make the model by making each part as a separate unit (body, hair, top, etc; this is the easier way) or the model as a whole. Study topology by looking at different models in MMD with wire frame enabled or by getting model source data and opening them in your 3D app. I always make the source data available for my parts. If you have a figma/figure, it can help you making better models. Also, disable perspective view when you start making your model as it will only interfere with your progress. You can (and should) re-enable it to check for topology faults that will affect the model in MMD (for example, face issues like Animasa Miku face)
The most important thing is to be not discouraged, whatever people will tell you.