The American Green Beret colonel who administered the spending of more than $100 million in U.S. military aid and the training of thousands of Salvadoran troops here in the past 15 months said today as he ended his tour that the guerrilla threat to El Salvador's government can be eliminated in two years.

But at a press conference this morning and in an interview yesterday Col. John D. Waghelstein, commander of the U.S. Military Group and all U.S. military advisers here, also outlined a long list of complexities and frustrations U.S. policy continues to face both in terms of the Salvadoran military's performance and U.S. backing.

U.S. strategy, as Waghelstein depicted it, intends to rebuild and restructure virtually the entire Salvadoran armed forces not only as a fighting unit but as the key political institution in the country. In effect the policy is supposed to combat one revolution--allied with Cuba and Nicaragua--by creating another one that is "controlled," as the colonel described it.

The most obvious aspect of the transformation in the Salvadoran Army is its projected expansion by 12,000 U.S.-trained soldiers, or 40 percent, in the next two years.

This morning Waghelstein was sharply critical of congressional aid cuts that stand in the way of such programs. He derided the "impatience" he called typical of "a lot of people in Congress" who say, "Where's the end?"

"We asked for $110 million, we got $55 million," he said, referring to reductions in this year's military assistance to El Salvador. "That means we're going to be able to do half of what we anticipated doing."

Asked how long it might take to eliminate the rebels as a threat to this government, Waghelstein said, "In two years, if the aid continues and the force expansion that we've got programmed continues, it's doable."

But Waghelstein's optimism is not based on tangible victories against the guerrillas.

Some inroads recently have been made against their Guazapa stronghold about 30 miles from the capital, but Waghelstein acknowledged that since his arrival here a week before the March 1982 elections the rebels, numbering from 6,000 to 7,000 combatants, have expanded their control in the country's northern provinces and until recently maintained a steady, debilitating offensive against the government.

The "progress across the board" he cited today is mainly within the government forces as they have faced U.S. demands that they change their tactics, their training programs, their promotion system, their attitudes about everything from the use of artillery to the widely reported abuse and murder of prisoners and suspected leftists.

In Waghelstein's view, the political and military aspects of the war are inextricably linked.

He endorsed the military leadership's self-proclaimed role as the "guarantors" of whatever democracy has developed here since an Oct. 1979 coup by younger officers ended a long dictatorship of general-presidents tied to an "official" political party.

"We have encouraged those who see this war in other than purely military terms," he explained.

While some officers continue to have partisan loyalties, the basic leadership has "staked out the political center," he said, although the most openly right wing of the senior officers, Nicolas Carranza, was recently given a sensitive and powerful position as commander of the feared Treasury Police.

"They're not all Jeffersonian democrats by any stretch of the imagination," Waghelstein said yesterday. But he added that most do take pride in their role "guaranteeing last year's elections" and assuring that "what came out of the elections survived."

Actually, when a rightist coalition with a majority of the votes attempted to take over the government on that basis last year the military stepped in to appoint its own more centrist civilian candidate as president.

Waghelstein was vague when it came to describing in concrete terms the improvements in the Army's performance on human rights. He said that more prisoners are being taken in combat--rather than killed on the spot--but could give no figures.

Instead, he talked about the "ambience" of violence that exists in this country regardless of the insurgency.

"I was driving to work yesterday and there was a stiff lying by the road in Escalon," an upper class neighborhood, Waghelstein said by way of illustration. He suggested there was no way to tell if the man, in civilian clothes, was killed for political reasons or because he was caught sneaking out somebody's back door.

Waghelstein did say of the Army, "Everybody's not clean. We know that." But he added that such extensive changes are under way that the institution will undergo radical, positive change in the next few years.

Waghelstein said that by the end of this fiscal year a total of 1,100 Salvadoran officer candidates will have been trained by the United States, which he said is more than have graduated from the Salvadoran military academy since it was founded in the 1930s.

Asked if this would be a destabilizing force in this country where young officers on the rise traditionally are coup makers, Waghelstein said yesterday, simply, "That's another problem that has to be dealt with."

The prime example of the new military strategy is an ambitious program under way in San Vicente and Usulutan provinces in which the Army is supposed to play a "supporting role," once it has forced out guerrilla concentrations, and "civic action" programs are expected to start.

"If you're looking for yardsticks don't look for body counts because that's not what the operation is about," said Waghelstein. Instead, look for statistics on acreage under cultivation or new schools being built, he said.

Critics of U.S. policy here tend to see a parallel with Vietnam in the way Washington has taken over the strategy and planning of the war effort and contend that the door is opening to escalation of the American presence.

The arrival of a 25-man U.S. military medical team Sunday, raising the total number of advisers operating here to about 80, was seen by many critics as a confirmation of this trend. But Waghelstein said that he does not contemplate the use of U.S. troops here unless it is to confront a Nicaraguan or other outside invasion.