I bought a Janome 300E used on ebay from a local person and it works great. I paid about $550. Hancock Fabric sells the 300E for $899. The 350E has some bells and whistles but I could not see a price around $1300 to have that much extra value.
The most important thing is to find out how you plan to use the machine, set a price point and then move forward. Wilcom has a free program that will convert most embroidery formats to the one used by your machine. The Janome uses JEF. The only transfer mechanism for designs you need is a compact flash (I use up to 512 Meg with no problem, just don't fill it up) and there is no extra expense for a transfer program.
Ebay has some great deals on thread - you can buy 5,000 or 10,000 yards for the price stores sell 1,000 yards. Of course, you will need a lot of colors which quickly adds up to $$