broken bolt in exhaust manifold

Replace manifold ......

-or-

Remove manifold and drill it out......

This is unfortunately a common problem for 5.4L engines. Persoanlly I'd raise hell with the dealer for a 3 year old truck. They might cut you a brake. THere is a TSB related to this problem. Partial text follows:

Exhaust System - Exhaust Manifold Studs Broken

TSB 05-5-4

USE OF STAINLESS STEEL EXHAUST STUDS IN SERVICE FOR 5.4L 2V ENGINE

FORD:

LINCOLN:

ISSUE Some vehicles equipped with the 5.4L 2-valve (non supercharged) engine, may exhibit broken exhaust manifold studs.

ACTION On the affected bank only, replace the exhaust manifold, manifold gasket(s), and install all new stainless steel exhaust manifold studs and nuts. Torque the studs in the cylinder head to 71-115 lb-in (8-13 N.m). Torque nuts on studs to 204-239 lb-in (23-27 N.m). Refer to Workshop Manual Section 313-01A for exhaust manifold removal and installation.

Ed