It is said that a cheap Porsche can be a lot more expensive than a well sorted one. If you have never had hands on one and taken it apart to see what makes it tick (usually a stuck lifter, but could be a lot worse), either buy one at market price with a good PPI, or buy one at a price that you will be okay if you part it out and scrap it. Like investing in the stock market, where you should put your money depends a lot on your risk tolerance.
I have bought many 986 Boxsters; fixed them, parted them, sold them, and kept them. A six speed transmission may be swapped into a five speed car, but you'd be better off just finding the right six speed car to begin with. The main complication is the axles being different, but other things need to be addressed too such as shift linkage, and clutch slave. An auto to manual swap is also technically possible, but way more trouble and expense than buying the right car to start with.
The last two I bought were the least expensive: A 2001 with a bad engine for $1,600 and a high mile 1997 for $2,500 with a hardtop. I put a failing engine in the $1,600 and
had some fun with it. The parts I've pulled off of it are worth well more than I paid. The
$2,500 car needs some work to make it fully functional and reliable, but it should be a good daily driver for what (to me) will be about $3,000 invested. Neither of these would have made any sense if I didn't already have lots of parts saved up and basic knowledge of how to work on THESE cars.
I'm as happy working on a Boxster as driving it. If you feel the same and have money to gamble with, go ahead and take some risk. There are a lot worse ways to lose money and waste time. If nothing else, buying a cheap Porsche can be a great education. Just be aware that it may not go well. One
guy on the GRM forum bought a beautiful but risky car and now has to make a tough choice. Rebuilds are not cheap on these cars. When an engine goes, there are often no good options.