Most of those questions require executive branch involvement to answer. Congress has the pocketbook and the executive branch has the planning. That's how it's always been and how it should always be. Go call Trump and have him tell DOT to get on it. Every agency in DOT has a master plan of what they want to do, based on conversations and feedback from local officials, and it's up to Congress to approve the funds. For example, the Federal Railroad Administration has an extremely comprehensive plan for revamping the northeast corridor, but it's not funded yet. And those priorities are usually based on requests from local officials at the county level. For example, Cecil County officials have been asking for a MARC and Amtrak station for a long time but the federal money has never come. Congressional reps are usually involved in these processes but the bill actually has to be brought up for discussion for details to come out.
Though I can tell you:
Determining the state by state allocation is 1. something that requires executive branch involvement and 2. something that would be hashed out through public hearings and amendments.
As for cost control methods, if the project goes out for a bid to private contractors, I believe the feds would have to pick the lowest qualified bid. That's usually how it goes. If it's done by government employees, they'd have a similar process for defining the scope and cost of the project prior to starting. I mean, there aren't really "methods" for controlling cost. There are mechanisms that encourage lower costs, but some things just cost a lot of money and infrastructure is one of those things.
As for being done "for the people, not political payback," that's just way to subjective to regulate. For a lot of projects, you could make an argument either way. Look at the TIF for Port Covington in Baltimore. You could say "oh, those developers donate a lot to pols. it's just payback." But in reality, Baltimore needs innovative economic development and a TIF may be the best way to achieve that for the people. You can make an argument either way. There's no mechanism or measure you can devise to eliminate any possibility or perception of "political payback." The mere idea of that is utopian. I mean, are you going to block funding for any project backed by a political donor or politician? Great. Say goodbye to the redevelopment of Sparrows Point, the pending redevelopment of Bainbridge in Cecil County, Port Covington, etc... It's just not wise to block funding on the perception of impropriety or corruption. This is is why we have elections. To elect representatives that know what their district needs and will fight for it. The only way to eliminate this perception of corruption is through campaign finance reform but the Supreme Court decided that money is speech, so we're fucked anyway.