Welcome to the whacky world of Arisaka. What has apparently happened is that your replacement stock is of a different Arsenal or variation than your receiver. The Japanese T-99 Arisaka was MFG at several different arsenals in Japan (plus one in Korea). And while one would think that all guns from any arsenal, being of same design, would have interchangeable parts. That's not always the case with the T-99. And differences often appear, especially in stock set swaps. I learned this the hard way myself.
The T-99 was purposely made with loose tolerances that varied slightly from arsenal to arsenal. Add into that mix the problems that the Japanese had in MFG as the war went on.
As the allies increasingly took control of the seas and skies around Japan, the Japanese had increasing problems getting war materials into Japan. Add to that Allied bombings of Japanese war industry. And the Japanese habit of drafting from their experienced labor force to fuel their insane Banzi charge waste of soldiers. The end result was a gradual decline of MFG quality of the T-99 rifle. To the point that the very robust early war T-99 by wars end was reduced to a low quality rifle of questionable safety to fire.
Generally there are 3 variations of the T-99. Early War (1940-42 vintage). Mid War "Transitional" (1943-early 44). And Late War "Last Ditch" (late 1944-45).
It would actually take quite alot to describe the the differences. But to adress your problem, you have IMO two options. The 1st and CORRECT option would be to obtain the correct Arsenal & variation stock set. There are a several of ways to determine this. the 1st being the stock Arsenal stamps. Located on the underside of the buttstock. One near the bottom of handgrip area. Another about 1/2 back towards the butt. These are often filled w/dirt/grime and commonly mistaken by unknowledgable people as stock dings. The 2nd is by the length of the Cleaning rod and the method of retraining it. Early war rifles had long rod. Mid War had a short rod. Late war had no rod. And 3rd is by stock color. Early war rifles generally had a HONEY BLONDE stock finish color. Which changed to to an orange reddish color around mid war.
If you use this web page to determine the Arsenal & Series of your T-99, I can help you determine what type of stock you need. If you cannot figure out the Arsenal/Series yourself, I may be able to if you post GOOD CLEAR pic of markings on left side receiver. Need ALL markings there. From the very small one just before serial number (Series mark) to the larger one after serial number (arsenal mark).
Finding the correct Arsenal/Series stock my be a challenge. But can be done. And once located you can very likely either swap with the owner (if he's a collector). Or resell the one you have to recoup costs. I would suggest going to the Japanase Collector forums at Gunboards.com to search. It is IMO the best Arisaka forum on the web.
Your other option is to modify the stock. Basically "Hand fit" it to your action. Most likely with a rat tail file to round out the action bolt holes until the screws are able to line up. I would discourage this. If I can be of further help, feel free to ask.
http://www.radix.net/~bbrown/japanese_markings.html
