My theory, feel free to poke holes in it :)
SA assaulted TH sometime after her arrival, took her to the nearby quarry, killed, and burned her body. The remains and bullet remained at the quarry. He returned to TH's car and towed the car to the location where the car was eventually discovered. By towing the car SA would not need access to the interior of the car. Thus explaining the lack of SA's fingerprints inside the car. As to the exterior, SA probably used a glove (as likely do most tow truck drivers) to ready the car for the tow. Once, the car was relocated, SA opened the hood, removed the battery cables, and license plates. He did not use the nearby car crusher, because even a crushed car would leave evidence (in fact the police did eventually search all the vehicles on the property). SA likely planned to remove the car from his property when the search was called off at a later date, thus he unhooked the car battery so that it would not die. In doing so he left DNA evidence inside the hood. He likely took of his gloves prior to opening the hood when he detached the car from the tow as he was accustomed to doing so (muscle memory). SA burns personal belongings in burn barrels.
On 11/3, Halbach's friends and family report TH as missing. The police are given her license plate number. Colborn discovers the car in advance of the offical discovery (11/5). Since, the license plates were missing he checks the vehicle identification number (VIN). The VIN revealed the year of the car, and exterior logos reveal that it is a Toyota Rav4. Colborn calls dispatch (11/3) and repeats license plate number (known to the police) and asks 99 Toyota? This confirmed that the VIN matched the missing plates. Colborn highly suspicious searches the area and discovers the remains of TH at the nearby quarry.
Colborn did not report/call in that he found the car or remains, because he was on the premises without a warrant and feared his discovery would be excluded/inadmissible at a subsequent trial. Further, this afforded him the opportunity to strengthen the case against SA (and thus diminish the civil case).
Colborn relocates TH's remains to the burn pit by SA's trailer. Colborn retains the bullet used to kill TH and the key from inside the car, which is later planted in SA's garage and trailer, respectively. Colborn later returns (maybe 11/4) with SA's blood retrieved from the blood vial in evidence (breaks tamper tape in the process). He plants SA's blood inside the car.
TH blood found at the back of the car was of an inconsequential amount that may of been the result of some unrelated earlier accident.