Hope this is of some help. I'm a Zen Monk and a swordsman of twenty years in a Koryu. The following was explained to me by Yoshiaki Unno Sensei, Senior Student of Minourou Mochizuki Sensei (comtempory and senior student of Ueshiba Sensei and Kano Sensei).
Traditionaly a Dojo is orintated East-West. The significance of this being that the Sun rises in the East this has Shinto relevance to do with the creation of Japan ect.
At the East end of the Dojo should be located the 'Kamidama' Lit. 'the gods place' usually the appropriate Shinto diety is enshrined here as per the art form taught/practiced in the Dojo. usualy this consisted of a raised dais 9which it's self is devided into Jodan - upper, and Gedan - Lower. In a Dojo this corespond to the main entrance to the Dojo being located on the North wall, hence Jodan to your left as you turn to the east, and Gedan to your right. Important guests are offered a sitting space near this point ect.
Insence may be offered and burnt here. If you whish to make a really authentic Kamidama for some reason you can do some searches on shinto shrines to get everything right
to suffice though a sinple Kanji may be hung at this end of the Dojo.Perhaps a flower arrangement. Depends how deep your training has been really.
Located at the West end of the the Dojo should be located the 'Butsudama' Lit.'place of Buddha' the significance relating to the Pureland teaching of ultimate rebirth in the Western Paridise. Butsudama may consist of a 'cuboard' in which incence is place and a small statue of some significance (Kwannon or a Buddha).
a dojo is usually from 18 mats up wards in size, the number of tatami determines it's volume, but smaller is known or school's corresponds to 18, which is pretty good for personal use, a bit squishy when it comes to classes unless like us you only accept a few trainees at a time.
as to hieght traditionally the cieling should be18 feet, high enough for a naginata, but if it dosen't bother you you can come down a bit to a hieght that allows a boktoh to be swung Jodan-Mae-Uchi safely.
a gravel courtyard is common, usually modelled on the compound of a shinto shrine or Buddhist temple, but grass ect. is fine
Traditionally the path leading to the Dojo (or house for that matter) should be from the South to North , here you get into aspects associated with traditional divination.
If you visit Japan you will find that Shrines, Temples, Castles, Dojos, worshops, houses, ect. are placed according to traditional aspects of divination rather than mere town planners!
Even the Aiki shrine was built like this
Hope that was of some help. If you need more email me firstname.lastname@example.org
or visit austkodo.org.au
hope that helps a bit.