Time to make a move.

What you described about the multiple branches radiating around the trunk, just below where the trunk has been top cut, is a typical growth pattern for such drastic top pruning. All too often growers have already done such pruning to larger crape myrtles when they are shipped to the retail nurseries. Did your area get the recent days' hard freeze around the Easter holiday? If so the CM in question might have a lot of dead wood which needs to be pruned out. If such a freeze happened, watch the tree as its remaining buds leaf out again. Once the tree appears to be fully leafing out enough to look recovered from any winter or freeze damage; totally remove any trunks or branches which fail to releaf. Also from the trunks nearest your house, completely remove all the way to the trunk any branches in the canopy which you can clearly tell will grow to infringe on your roof. Throughout the following growing seasons feed the tree with slow release quality food, and after every week which fails to provide an inch of rain for the shrub, suppliment the tree with that much water. Over the summer let the tree bloom naturally, and do not prune off the resulting seeds in an effort to extend your bloom season to the first freeze of late fall or early winter. By letting the tree bloom by itself and by being patient if it seems to slow down in bloom presentation after the first bloom flush; the tree will be enabled to put forth effort into thickening its branches and developing its proper rooting perportions. After the tree goes dormant, depending on when temps drop low enough for that, consider the space which any branching from the trunks still invade your roof line. cut, at that time, each trunk, all the way down to the root ball, whose canopy clearly will grow to infringe on your roof line. Hopefully when you have accomplished all the above pruning you will end up with the best of either a one or three main leader trunks. Then, in early march of the next year, prune out again all brittle dead wood, brake off the remaining seed pods and their twigs. Then turn your focus onto any remaining radiating branches which are growing just beneath the previously described, chopped off trunks. Preserve only a flexible and clearly healthy branch which grows the most directly upward and toward the direction where you want the trunk to continue growing. Prune away any other branches which are growing around the trunk near the same level of the healthy upward growing branch you selected to retain. To repeat: the one branch you choose to keep growing off the end of such chopped off trunks should be the one out of the ratiating bunches which appeares to be growing most upright, and growing in the right direction for the retained branch to assume the role of developing into a continuation of the trunk. Hopefully each single branch you select to continue the remaining trunks are thick enough to survive the following winter freezes. If not you will need to wrap each and their tunks with cotton insulator wrap prior to each freeze. If the temps are forecast to drop down to a hard freeze than add bubble wrap around the cotton wrap. Just be sure to remove the plastic bubble wrap any time the temps rise back up above 33 F. degrees. The above advised action takes a lot of dilligent effort, so if you do not think the tree is worth the trouble, simply remove it, grind the stump and main roots and purchase a 10 to 15 gallon sized, 25 to 30 feet potential height grower Crape Myrtle which has not also already been such drastically top pruned-down by the grower. With any such new CM tree you plant in the area, make certain to plant it far enough from the house to prevent roof damage, and to also prune train it properly each year just as you first described above.

Yes, anything without green at this point is dead and can be pruned away. Take that 4th trunk all the way to the ground if it is sprouting at the base. Was it colder than usual at some point this winter? I know here in Atlanta we got down to 10 degrees which is the lowest temp in our range.

No, in fact NO, it's NOT the way they are pruned - it's the variety. There are CM cultivars that grow no taller than 3' and those that grow to 35' or more. If you REALLY have fallen in love with one of the huge ones, and have a smallish space for it, you MIGHT get away with keeping it multi-trunked, and cutting out about a third or less of the trunks every few years, but you would have MUCH less trouble if you decided that you do like one that will mature at the desired size. Pruning for shape and health - crossing, broken or wayward branches - on CMs should be done in late Jan. or Feb. If you want to prune out suckers from the trunks or roots, then do that in mid-summer, as they are less likely to resprout then.