They are not built on the same block, but a swap is possable. The 4L60E is the backbone of chevy, with almost any engine being able to bolt to it. You will need a new bell housing though. Also, the swap will require a new custom wiring harness for the LT1. Also, the LT1 donor engine has to be of the same year or newer to be smog legal. You might be able to find one in a junk yard, or more likely at a insurance auction. Ask your insurance company, or any other one for that matter to keep a lookout for a insurance totaled 99-01 Vette. If one is not forthcoming you can apply for a CARB exemption with the Secretary of State in your state. Good luck if you live in Clafornia.
Also, your Whipple charger will most likely not fit on the LS1 without a custom manifld.
It would be much more cost effective to increase the performance of your current truck. You can increase the output of the whipple with a smaller pully. But if you dot hat you will need High performance injecters as your truck is prolly starved already with the hyper-efficent Whipple. you could also install a port injected NOX kit. These are available through many retaillers like Jegs. ( jegs.com ) Model # 741-05088 this kit can get you into the 10's with the full 300 Hp increase. You will need to upgrade to Forged pistons though for durability reasons. Also think about headers. you can gain another 50 HP or so if you get the right ones. Talk to some people online who have your truck or one like it to see some ideas. Make sure that your headers are ceramic coated for heat disapation and long life.