1.After Gates and Allen found some success selling their programming language...

你要掌握一个原则，分词作宾补，分词的逻辑主语必须是宾语。分词作状语，分词的逻辑主语为句子的主语。所以这里selling不可能是宾补！！！ 分词为状语，不要管是什么状语（时间状语）。

2.Allen also funded maverick aerospace designer Burt Rutan's SpaceShipOne,which in 2004 became the first privately developed manned spacecraft to reach space.

manned spacecraft 载人飞船是个合成名词，privately developed为过去分词作前置定语（私人开发的）。

3.What he always seemed to lack,Enderle said,was another Bill Gates to help fulfill his visions.

这一句话改写成 Enderle said(that)what he always seemed to lack was another Bill Gates to help fulfill his visions 可以吗？

原句为自由间接引语。引语作了主句，引述分句为插入语。

你改写的句子引述分句为主句，引语为宾语从句。意思相同，侧重点不同。