Once again, I am very familiar with your type of setup and I'm sure it worked out just fine for you... look at his first post, his great description was "stock fuel"... you can run stock fuel (injectors, rail, pump, etc.) and have a SAFC (known as fuel/engine management)... I just wanted to make sure I had a complete understanding of his current setup...
And if you wana get nit-picky, the LS400 maf is not "stock" fuel management
Now ASSuming you havn't put anything on the car for fuel management, it sounds like your car is running in limp mode (is there any black smoke comming out of the exhaust?)
Also, and I know you've already done this, really go over all your vac lines and be sure they're good... after that, check your MAF and make sure the connection is good there as well as the rest of your electrical connections...