Id do it ! I'm in the making of doing an E2 out of Thomas, so I'd say go for it! Be sure to be careful as rushing it can ruin the final product as I have done before, so be sure to take your time. Everything wrong sounds like a simple fix. The side rods can be fixed with a dab of plastic glue just be sure not to get it anywhere else in the wheel, as it can get the rods stuck. The coupler from Henry to the tender can have 2 ways of being simply and cheaply fixed. One is electrical tape surrounding the whole coupler. Next try normal couplers, but one preferably larger than the normal ones, like Trackmaster Scruffs who's coupler is large than normal ones as collision of the tender or car to the engine can cause slower movement on turns and constant derailments. Hope it works out

From Thomas To Today's Modern Diesels, They're All A Part Of My Rail-Yard!