301 redirect from mysite.com to MIVA store (store.mysite.com) will it affect page rankings

[Iris]

Hello,
I have a regular site (mysite.com) which I am moving from a windows server to a linux server. The extension will change from .htm to .shtml or .php
We are doing this so we can use css and server side includes to clean up the code for better SEO. We will also be adding a blog.
We plan to use 301 redirects because of the server and extension change.
This site has been up for 12 years and gets Google page ranks of mostly 2-3. It has around 6000 natural back links.

We also have a MIVA store (store.mysite.com) which has been up since 2006 but has poor Google Page Rankings 0-1.
We have order buttons on mysite.com which take the customers to the MIVA site.
It has been suggested that we   discontinue the original mysite.com and use just the MIVA store with 301 redirects from mysite.com to send the backlinks and traffic to the Miva store. But we are very concerned about losing page rankings from mysite.com.if we no longer have mysite.com and just have the MIVA store.
Can anyone advise us on whether the 301 redirects will bring all the page rankings to store.mysite.com (MIVA site)
The other concern is the coding on MIVA. We are worried that the coding will hinder the search engine spiders, especially since it does not have good page rankings after being live for 6 years.
Overall, I think that we should keep the original site and continue using order buttons on the original site to send customers to the MIVA store to purchase products so we do not lose the page rankings of the orignal mysite.com
It is a lot of work to maintain 2 sites but if we lose our rankings, it would be terrible.
This is a big and scary decision to make and any advice would be appreciated.
Thank you, Iris

[Daniel Perri]

You don't need to use redirects for a sever change just a DNS mod.

Cleaning up the code with includes won't help seo.

And why are you moving from windows to Linux. You can use PHP on a windows machine but can't use asp.net on a linux server. You also can't use mssql. It seems like you are limiting you're options and taking a step backwards. Search engines don't care which server os you use.

As far as redirects for page moves you should use a 301 permanent redirect or 302 if it is temporary

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