How long is the proposed scheme and how big is your design team?

I would list the most important factors affecting it's cost to construct e.g. land cost, materials and specialist equipment availability and seek to minimise them.

For example, in the UK we are tight for land and have taxes imposed for dumping materials to landfill, therefore we concentrate on minimising the cross-section and optimising the cut/fill balance. We also have to factor in the future economic performance, e.g. delays to travellers, etc. something which may not be as important (at present) in southern Africa.

What are the primary factors which will affect your construction and future operating costs?

I would highly recommend that you review the AASHTO Geometric Design of Highway and Streets (or "Green Book").  Pages 229-231 (2004 version) discuss the general design controls for horizontal and vertical road alignments as individual design aspects.   Pages 280-285 discusses the importance of "harmonizing" the vertical and horizontal alignments - this is something I see few engineers adhere to, and it is a very important section to consider when designing a new road.

Since you're in one of the bits of the world that used to be coloured pink, you might also need to refer to DMRB;

http://www.standardsforhighways.co.uk/dmrb/index.htm

In South Africa you'd have to do an Environmental Impact Assessment.  Does Swaziland make you do the same?  Choosing a road alignment does not only need to consider road geometrics, but also needs to be determined with consultation of the community. You need to have a strong handle on drainage, too, or your road will erode or cause severe erosion if you concentrate flow in new locations. It's one thing if you have a defined corridor in which to finalise horizontal and vertical geometrics, but quite another if you're looking at virgin mountaintop and are wondering where to draw your line.

Debaser, South Africa follows AASHTO, so I imagine Swaziland does too.  

Thanks for the input.  I have only been asked to sub-contract the geometric design portion of 50km in Lesotho, but have been asked to provide a methodology on identifying possible alignment corridors and then finalizing a suitable alignment.

I have no problem with the design standards (in Swaziland we are not restricted to any standard, but generally use South African (TMH, TRH series) but to be honest i have not seen the AASHTO green book (does anyone know if it is readily available in SA?) but all the others i have seen seem to be pretty similar.  i am awaiting confirmation, but imagine that Lesotho is also not fixed on any specific standard so long as it has international accreditation

You should be able to buy the Green Book online. https://bookstore.transportation.org/Item_details.aspx?id=110

I suppose it's not promising that the Lesotho minister for public works and transportation's email address is a yahoo.co.uk address. http://www.lesotho.gov.ls/works/minister.php I almost want to send him one of those Nigerian spam emails. At least the CIO has an official email. http://www.lesotho.gov.ls/works/contacts.php I would highly recommend calling them and discussing their standards/expectations.