don't know about the brakes but for the trans whine let me ask you this.....
does the trans only make the whine in 1st and 2nd gear then goes away?
if the answer is yes, it is a known problem, see below
FORD:
2001-2003 EXPLORER SPORT TRAC, EXPLORER SPORT, RANGER
ISSUE:
Some 2001-2003 Rangers, 2001-2003 Explorer Sport/Sport Trac, built prior to 10/18/2002, equipped with a 5R55E automatic transmission and 4.0L engine, may exhibit a gear whine type of noise in 1st and 2nd gear ONLY. This may be caused by the Reverse and Forward Planetary assemblies and/or the driveshaft.
ACTION:
Verify that only these conditions exist and no DTCs are present. If other conditions are present and DTCs exist they must be diagnosed and serviced first. Once all other conditions are serviced and only the 1st and 2nd gear whine are still present, refer to the following Service Procedure. Using the chart provided, select the parts that need to be replaced.
NOTE: IF PLANETARIES ARE LISTED, BOTH MUST BE REPLACED.
SERVICE PROCEDURE
Gear Whine Service Procedure
1. Determine whether the driveshaft only, planetaries only or both driveshaft and planetaries need to be replaced, refer to Application and Component replacement chart.
2. If just the driveshaft needs to be replaced follow the procedures as listed in the appropriate Workshop Manual section for driveshaft removal/replacement.
3. If the planetaries need to be replaced, using the appropriate model and year Workshop Manual, Section 307-01, Transmission Removal procedures, remove the transmission.
4. Discard the driveshaft ONLY if being replaced. Refer to application and component replacement chart.
NOTE: REPLACEMENT OF THE EXTENSION HOUSING SEAL AND BUSHING ARE NOT REQUIRED. DO NOT DISASSEMBLE BEYOND THE REVERSE PLANETARY. ALL SUBASSEMBLY STEPS ARE NOT REQUIRED FOR THIS PROCEDURE.
NOTE: BOTH PLANETARIES MUST BE REPLACED OR THE REPAIR MAY NOT BE EFFECTIVE.
5. Using the Transmission Disassembly procedures remove the Forward Planetary Assembly (7A398) and the Reverse Planetary Assembly (7D006) and discard. Do not disassemble beyond the Reverse Planetary assembly.
6. Using the appropriate Transmission Assembly procedures, assemble the transmission and install BOTH NEW service Reverse Planetary Assembly (XL2Z-7D006-AA) and a new service Forward Planetary Assembly (XL2Z-7A398-AA).
7. Using the appropriate model and year Workshop Manual, Section 307-01, Transmission Installation procedures, install transmission.
8. If being replaced, Install the NEW service driveshaft 2L2Z-4602-AA as required for the appropriate application listed.
9. Verify repair. Clear DTCs.